FasterDB - Main

		Gene
Symbol		SEC61A2
Synonyms		FLJ10578
Description		Sec61 alpha 2 subunit (S. cerevisiae)
EnsEMBL link		ENSG00000065665
Chromosome		10 - forward strand
Chromosomal location (UCSC link)		12171640 - 12211956 (40317bp)
Sequence		sequence
Associated transcripts		NM_001142627 NM_001142628 NM_018144 AK301841 AK292295 BC026179 AF346603 AK057532 AK022640 AK022027 CR607709 AK001440

		Alternative 3' splice site (acceptor)
Identifier	Position	Distance (bp)	Transcript

		Alternative 5' splice sites (donor)
Identifier	Position	Distance (bp)	Transcript

	Intron retentions
Identifier	Position	Transcript

	Exon deletions
Identifier	Position	Transcript
No data

	Transcription start sites
Identifier	Position	Gene coordinates	Chromosomal coordinates	Transcript
P1	1	1	12171640	NM_001142627 NM_001142628 NM_018144
P2	1	48	12171687	AK301841
P3	1	51	12171690	AK292295
P4	1	60	12171699	AK057532
P5	1	66	12171705	AK022640
P6	8	26146	12197785	AK022027
P7	9	27269	12198908	AK001440

Protein prediction
Transcript name	Sequence
NM_001142627	sequence
NM_001142628	sequence
NM_018144	sequence
AK301841	sequence
AK292295	sequence
BC026179	sequence
AF346603	sequence
AK057532	sequence
AK022640	sequence
AK022027	sequence
CR607709	sequence
AK001440	sequence

	Polyadenylation
Identifier	Position	Gene coordinates of cleavage site	Chromosomal coordinates of cleavage site	Pattern	PolyA tail	Accession number	Type
PA1	13	34947	12206586		no	AK301841	Full_length
PA2	13	35187	12206826	AATAAA	no	AK022027	Full_length
PA3	13	35187	12206826	AATAAA	no	AK001440	Full_length
PA4	13	35764	12207403	AATAAA	no	NM_001142628	Cdna
PA5	13	35764	12207403	AATAAA	no	NM_018144	Cdna
PA6	15	40317	12211956	AATAAA	yes	NM_001142627	Cdna
PA7	15	40317	12211956	AATAAA	yes	BC026179	Cdna
PA8	15	40317	12211956	AATAAA	no	AK022640	Full_length
PA9	15	41608	12213247	ATTAAA	no	DB315342	3prime_est

More polyadenylation sites ...

	Exon skipping
Identifier	Position	Transcript
ES1	3	NM_001142628 AK301841
ES2	4	NM_001142627 NM_001142628 NM_018144 AK301841 AK292295 BC026179 AF346603 AK022640
ES3	13	NM_001142627 BC026179 AK057532 AK022640
ES4	14	NM_001142627 AK022640

	Splice site strength
Identifier	Site	Exon	Strength	Alternative	Sequence
S1	5' (donor)	1	7.39	no	GCAgtgagt
S2	5' (donor)	2	9.72	no	AAAgtaagt
S3	3' (acceptor)	2	9.15	no	tattatttttctttttacagTCA
S4	5' (donor)	3	9.8	no	CAGgtatgt
S5	3' (acceptor)	3	8.11	no	ctttacattttgttgtacagATC
S6	5' (donor)	4	7.46	no	CAGgtataa
S7	3' (acceptor)	4	8.34	no	cttcttccatgttattacagATT
S8	5' (donor)	5	9.12	no	GAGgtatgc
S9	3' (acceptor)	5	8.97	no	tattttgtgtactattttagATC
S10	5' (donor)	6	6.06	no	AACgtgagc
S11	3' (acceptor)	6	13.5	no	tctctccccttcctttccagGAA
S12	5' (donor)	7	10.77	no	CAGgtaaga
S13	3' (acceptor)	7	6.23	no	ttccccccaactttcatcagTGT
S14	5' (donor)	8	6.75	no	GAGgtacat
S15	3' (acceptor)	8	10.77	no	ttgcatttctttccccacagTTG
S16	5' (donor)	9	10.08	no	CAAgtaagt
S17	3' (acceptor)	9	12.19	no	tgtctgtcttgattttacagGTA
S18	5' (donor)	10	8.56	no	GCCgtgagt
S19	3' (acceptor)	10	13.63	no	ctctccgtttccttttttagGGA
S20	5' (donor)	11	9.11	no	GATgtaagt
S21	3' (acceptor)	11	8.56	no	tttgtactcctgttctgtagGAT
S22	5' (donor)	12	9.31	no	TAGgtaagg
S23	3' (acceptor)	12	10.17	no	agtcgtttttctctcggcagGTA
S24	5' (donor)	13	-10.73	no	ATTaaacgt
S25	3' (acceptor)	13	8.99	no	cttggggttctgtctcctagGTA
S26	5' (donor)	14	7.64	no	CAGgtacta
S27	3' (acceptor)	14	6.54	no	tttgcatttgcatgtttcagTGC
S28	3' (acceptor)	15	7.74	no	ttttttctcccttttctaagACC

	Conserved exons
Gene identifier mouse	Position human	Position mouse
11395	1	1
11395	2	2
11395	3	3
11395	5	4
11395	6	5
11395	7	6
11395	8	7
11395	9	8
11395	10	9
11395	11	10
11395	12	11
11395	13	12

Report
Exon	Number of supporting transcripts
Transcription initiation & first exon(s)
1	5
8	1
9	1
Transcription termination & last exon(s)
13	5
15	4
Exon skipping
3	2
4	8
13	4
14	2

Splicing factors
Splicing factor	Exon array	CLIP data	Exon position
CELF1 (CUG-BP)
DAZAP1
ELAVL1 (HuR)	Yes	Yes
ESRP1/2 (ESRP)	Yes
FUS		Yes
HNRNPA1		Yes
HNRNPA2B1		Yes
HNRNPAB
HNRNPC		Yes
HNRNPF/HNRNPH1	Yes	Yes
HNRNPL	Yes
HNRNPL_2
HNRNPM		Yes
HNRNPU		Yes
MBNL
NOVA1
PTBP1/2 (PTB)	Yes	Yes
QKI
RBFOX2 (FOX2)		Yes
RBM4	Yes
SFRS3 (SRP20)
SFRS6 (SRP55)
SFRS7 (9G8)
SRSF1 (SF2ASF)
SRSF2 (SC35)
SRSF5 (SRP40)
TDP43
TIA1/TIAL1		Yes
TRA2A
TRA2B
YBX1 (YB1)

	Expression
Exon position	Tissues	Cell lines	Cancer cell lines
1	Expression	Expression	Expression
2	Expression	Expression	Expression
3	Expression	Expression	Expression
4	Expression	Expression	Expression
5	Expression	Expression	Expression
6	Expression	Expression	Expression
7	Expression	Expression	Expression
8	Expression	Expression	Expression
9	Expression	Expression	Expression
10	Expression	Expression	Expression
11	Expression	Expression	Expression
12	Expression	Expression	Expression
13	Expression	Expression	Expression
14	Expression	Expression	Expression
15	Expression	Expression	Expression

	Exon-Intron
Position	Type	Gene coordinates	Chromosomal coordinates	Length	Sequence	Features
1	Exon	1 - 154	12171640 - 12171793	154	sequence	download
1	Intron	155 - 3600	12171794 - 12175239	3446	sequence	-
2	Exon	3601 - 3668	12175240 - 12175307	68	sequence	download
2	Intron	3669 - 6464	12175308 - 12178103	2796	sequence	-
3	Exon	6465 - 6530	12178104 - 12178169	66	sequence	download
3	Intron	6531 - 12792	12178170 - 12184431	6262	sequence	-
4	Exon	12793 - 12925	12184432 - 12184564	133	sequence	download
4	Intron	12926 - 13476	12184565 - 12185115	551	sequence	-
5	Exon	13477 - 13555	12185116 - 12185194	79	sequence	download
5	Intron	13556 - 19954	12185195 - 12191593	6399	sequence	-
6	Exon	19955 - 20086	12191594 - 12191725	132	sequence	download
6	Intron	20087 - 20211	12191726 - 12191850	125	sequence	-
7	Exon	20212 - 20321	12191851 - 12191960	110	sequence	download
7	Intron	20322 - 26137	12191961 - 12197776	5816	sequence	-
8	Exon	26138 - 26291	12197777 - 12197930	154	sequence	download
8	Intron	26292 - 27266	12197931 - 12198905	975	sequence	-
9	Exon	27267 - 27427	12198906 - 12199066	161	sequence	download
9	Intron	27428 - 28267	12199067 - 12199906	840	sequence	-
10	Exon	28268 - 28465	12199907 - 12200104	198	sequence	download
10	Intron	28466 - 31289	12200105 - 12202928	2824	sequence	-
11	Exon	31290 - 31481	12202929 - 12203120	192	sequence	download
11	Intron	31482 - 32572	12203121 - 12204211	1091	sequence	-
12	Exon	32573 - 32649	12204212 - 12204288	77	sequence	download
12	Intron	32650 - 34627	12204289 - 12206266	1978	sequence	-
13	Exon	34628 - 35764	12206267 - 12207403	1137	sequence	download
13	Intron	35765 - 38112	12207404 - 12209751	2348	sequence	-
14	Exon	38113 - 38253	12209752 - 12209892	141	sequence	download
14	Intron	38254 - 39617	12209893 - 12211256	1364	sequence	-
15	Exon	39618 - 40317	12211257 - 12211956	700	sequence	download

	5' untranslated regions
	UTR 1	UTR 2	UTR 3	UTR 4	UTR 5
Supporting GenBank accession identifers	NM_001142627 NM_001142628 NM_018144 BC026179	AK301841	AK292295	AK022640	AK057532 AF346603
Length	147	100	97	82	380
Number of ATGs in frame	0	0	0	0	0
Total number of ATGs	0	0	0	0	2
Number of GTGs in frame	0	0	0	0	3
Total number of GTGs	3	1	1	1	6
Number of CTGs in frame	0	0	0	0	1
Total number of CTGs	0	0	0	0	6
Number of micro ORFs in frame	0	0	0	0	0
Total number of micro ORFs	0	0	0	0	2
GC percentage	77	75	75	74	47
Number of pyrimidine tracks	0	0	0	0	0

	3' untranslated regions
	UTR 1	UTR 2	UTR 3
Supporting GenBank accession identifers	NM_001142628 NM_018144 CR607709 AF346603 AK022027 AK001440 AK292295 AK301841	BC026179 AK057532	NM_001142627 AK022640
Length	950	828	630
Number of ATGs in frame	2	3	3
Total number of ATGs	15	10	8
Number of GTGs in frame	5	5	4
Total number of GTGs	20	19	15
Number of CTGs in frame	5	3	0
Total number of CTGs	17	10	5
GC percentage	40	42	43
Number of pyrimidine tracks	7	2	2

	miRNAs
Identifier	Name	Gene coordinates	Chromosomal coordinates	Prediction algorithm
Group 1
M1	hsa-miR-204	34830 - 34851	12206469 - 12206490	miranda
M2	hsa-miR-211	34830 - 34851	12206469 - 12206490	miranda
M3	hsa-miR-204	34844 - 34851	12206483 - 12206490	pictar
M4	hsa-miR-204	34844 - 34850	12206483 - 12206489	pita
M5	hsa-miR-204	34844 - 34852	12206483 - 12206491	targetscan
M6	hsa-miR-211	34844 - 34850	12206483 - 12206489	pita
M7	hsa-miR-211	34844 - 34852	12206483 - 12206491	targetscan
M8	hsa-miR-211	34844 - 34851	12206483 - 12206490	pictar
M9	hsa-miR-520h	34854 - 34860	12206493 - 12206499	pita
M10	hsa-miR-520g	34854 - 34860	12206493 - 12206499	pita
Group 2
M1	hsa-miR-155	34976 - 34982	12206615 - 12206621	pita
M2	hsa-miR-885-3p	34987 - 34994	12206626 - 12206633	pita
M3	hsa-miR-124a	34991 - 34998	12206630 - 12206637	pictar
M4	hsa-miR-30a-5p	35006 - 35013	12206645 - 12206652	pictar
M5	hsa-miR-30e-5p	35006 - 35013	12206645 - 12206652	pictar
M6	hsa-miR-30d	35006 - 35013	12206645 - 12206652	pictar
M7	hsa-miR-30c	35006 - 35013	12206645 - 12206652	pictar
M8	hsa-miR-30b	35006 - 35013	12206645 - 12206652	pictar
M9	hsa-miR-338-3p	35033 - 35057	12206672 - 12206696	miranda
M10	hsa-miR-124a	35042 - 35049	12206681 - 12206688	pictar
M11	hsa-miR-338-3p	35050 - 35056	12206689 - 12206695	pita
M12	hsa-miR-433	35072 - 35093	12206711 - 12206732	miranda
M13	hsa-miR-19a	35102 - 35125	12206741 - 12206764	miranda
M14	hsa-miR-19b	35102 - 35125	12206741 - 12206764	miranda
M15	hsa-miR-19b	35118 - 35124	12206757 - 12206763	pita
M16	hsa-miR-19a	35118 - 35126	12206757 - 12206765	targetscan
M17	hsa-miR-19a	35118 - 35124	12206757 - 12206763	pita
M18	hsa-miR-19b	35118 - 35126	12206757 - 12206765	targetscan
M19	hsa-miR-1305	35159 - 35165	12206798 - 12206804	pita
M20	hsa-miR-454	35168 - 35191	12206807 - 12206830	miranda
M21	hsa-miR-429	35177 - 35201	12206816 - 12206840	miranda
M22	hsa-miR-200c	35179 - 35201	12206818 - 12206840	miranda
M23	hsa-miR-200b	35180 - 35201	12206819 - 12206840	miranda
Group 3
M1	hsa-miR-491-5p	35277 - 35294	12206916 - 12206933	miranda
M2	hsa-miR-186	35515 - 35538	12207154 - 12207177	miranda
M3	hsa-miR-384	35628 - 35651	12207267 - 12207290	miranda
M4	hsa-miR-30c	35647 - 35670	12207286 - 12207309	miranda
M5	hsa-miR-30b	35648 - 35670	12207287 - 12207309	miranda
M6	hsa-miR-361-5p	35741 - 35763	12207380 - 12207402	miranda
Group 4
M1	hsa-miR-873	39755 - 39776	12211394 - 12211415	miranda
M2	hsa-miR-125b	40156 - 40179	12211795 - 12211818	miranda
M3	hsa-miR-125a-5p	40156 - 40179	12211795 - 12211818	miranda

	Protein features
Category	Feature identifier	Feature name	Exons	Start on gene	End on gene
Binding	EXONT:001885	Protein binding	13	34758	34787
Localization	EXONT:000071	Transmembrane_helix	3,5	6486	13500
Localization	EXONT:000071	Transmembrane_helix	6	19957	20025
Localization	EXONT:000071	Transmembrane_helix	6,7	20086	20273
Localization	EXONT:000067	Nuclear_export_signal	7	20283	20321
Localization	EXONT:000071	Transmembrane_helix	7,8	20286	26170
Localization	EXONT:000071	Transmembrane_helix	8	26192	26254
Localization	EXONT:000071	Transmembrane_helix	9,10	27371	28279
Localization	EXONT:000071	Transmembrane_helix	10	28337	28417
Localization	EXONT:000071	Transmembrane_helix	11	31377	31463
Localization	EXONT:000071	Transmembrane_helix	12,13	32642	34769
Localization	EXONT:000016	Peroxisome targeting signal	14	38114	38122
Structure	EXONT:000071	Transmembrane_helix	3,5	6486	13500
Structure	EXONT:000071	Transmembrane_helix	6	19957	20025
Structure	EXONT:000071	Transmembrane_helix	6,7	20086	20273
Structure	EXONT:000071	Transmembrane_helix	7,8	20286	26170
Structure	EXONT:000071	Transmembrane_helix	8	26192	26254
Structure	EXONT:000071	Transmembrane_helix	9,10	27371	28279
Structure	EXONT:000071	Transmembrane_helix	10	28337	28417
Structure	EXONT:000071	Transmembrane_helix	11	31377	31463
Structure	EXONT:000071	Transmembrane_helix	12,13	32642	34769
PTM	EXONT:000797	Ubiquitinylated lysine	2	3603	3605
PTM	EXONT:000797	Ubiquitinylated lysine	2	3621	3623
PTM	EXONT:000162	O-phospho-L-threonine	6	19957	19959
PTM	EXONT:000161	O-phospho-L-serine	6	19978	19980
PTM	EXONT:000162	O-phospho-L-threonine	6	19990	19992
PTM	EXONT:000161	O-phospho-L-serine	6	19993	19995
PTM	EXONT:000797	Ubiquitinylated lysine	6	20053	20055
PTM	EXONT:000797	Ubiquitinylated lysine	10	28292	28294
PTM	EXONT:000797	Ubiquitinylated lysine	11	31476	31478
PTM	EXONT:000797	Ubiquitinylated lysine	12	32579	32581
PTM	EXONT:000797	Ubiquitinylated lysine	12	32588	32590
Unclassified	EXONT:009811	SecY subunit domain	2,3,4,5,6,7,8,9,10,11,12,13,15	3612	39621
Unclassified	EXONT:008748	Translocon Sec61/SecY, plug domain	3,5,6	6507	19956