FasterDB - Main

		Gene
Symbol		Traip
Synonyms		Trip
Description		TRAF-interacting protein Gene
EnsEMBL link		ENSMUSG00000032586
Chromosome		9 - forward strand
Chromosomal location (UCSC link)		107852467 - 107874599 (22133bp)
Sequence		sequence
Associated transcripts		BC006929 U77844 AK012948 NM_011634 AK040001 BC017374 AK012786

		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
IR1	9	BC006929
IR2	10	BC006929
IR3	11	BC006929

	Exon deletions
Identifier	Position	Transcript
No data

	Transcription start sites
Identifier	Position	Gene coordinates	Chromosomal coordinates	Transcript
P1	1	1	107852467	BC006929
P2	2	826	107853292	U77844
P3	2	828	107853294	AK012948
P4	2	832	107853298	AK040001
P5	2	846	107853312	AK012786

Protein prediction
Transcript name	Sequence
BC006929	sequence
U77844	sequence
AK012948	sequence
NM_011634	sequence
AK040001	sequence
BC017374	sequence
AK012786	sequence

	Polyadenylation
Identifier	Position	Gene coordinates of cleavage site	Chromosomal coordinates of cleavage site	Pattern	PolyA tail	Accession number	Type
PA1	1	197	107852663	AATAAA	no	BY635354	3prime_est
PA2	5	8352	107860818		no	AK040001	Full_length
PA3	18	21392	107873858	AATAAA	no	AK012786	Full_length
PA4	18	22133	107874599	AATAAA	no	NM_011634	Cdna
PA5	18	22133	107874599	AATAAA	no	AK012948	Full_length

More polyadenylation sites ...

	Exon skipping
Identifier	Position	Transcript
ES1	5	BC006929 U77844 AK012948 NM_011634 BC017374 AK012786
ES2	14	U77844 AK012948 NM_011634 BC017374 AK012786

	Splice site strength
Identifier	Site	Exon	Strength	Alternative	Sequence
S1	5' (donor)	1	9.46	no	CAGgtatga
S2	5' (donor)	2	10.13	no	ATGgtgagt
S3	3' (acceptor)	2	9.06	no	actgtgtctgtcgctggcagCTG
S4	5' (donor)	3	11.08	no	CAGgtaagg
S5	3' (acceptor)	3	8.97	no	tcattctgttttcactgtagCCT
S6	5' (donor)	4	7.87	no	AAGgtacat
S7	3' (acceptor)	4	10.69	no	tgtctcattttctcatccagGTT
S8	5' (donor)	5	-14.78	no	ATCttaaag
S9	3' (acceptor)	5	8.28	no	cttccttccattctcactagTCA
S10	5' (donor)	6	11	no	AAGgtaagt
S11	3' (acceptor)	6	9.67	no	gtatgtgcattgtcttgcagAAT
S12	5' (donor)	7	9.72	no	AAAgtaagt
S13	3' (acceptor)	7	8.64	no	cccctctgcttctgctccagACA
S14	5' (donor)	8	7.39	no	GCAgtgagt
S15	3' (acceptor)	8	8.39	no	gtcttgtgcttattcttcagAAA
S16	5' (donor)	9	4.88	no	GAAgtgcgt
S17	3' (acceptor)	9	3.7	no	gggccgggaatgtttttcagAAT
S18	5' (donor)	10	6.64	no	AAGgtgact
S19	3' (acceptor)	10	6.78	no	ttctcatggctgctttgcagAGA
S20	5' (donor)	11	8.94	no	ACGgtgaga
S21	3' (acceptor)	11	10.2	no	tggcttctcctttcttacagTTG
S22	5' (donor)	12	6.36	no	GAGgtttgt
S23	3' (acceptor)	12	10.61	no	tctcgctctcctttctccagAGC
S24	5' (donor)	13	11.81	no	ACGgtaagt
S25	3' (acceptor)	13	7.51	no	gatattttgtctgccttcagCCC
S26	5' (donor)	14	6.9	no	TTGgtgagg
S27	3' (acceptor)	14	9.79	no	tcctcttattccctcttcagCTG
S28	5' (donor)	15	10.19	no	CCGgtaagg
S29	3' (acceptor)	15	11.16	no	tctcctgtctcgtctcacagCTC
S30	5' (donor)	16	6.46	no	GTGgtgcgt
S31	3' (acceptor)	16	7.18	no	ctctggcattattccaacagGAG
S32	5' (donor)	17	-3.5	no	CCTgtatcc
S33	3' (acceptor)	17	12.7	no	catctcttccctctccctagGTA
S34	3' (acceptor)	18	5.91	no	ttccttgacattgcttccagAGG

	Conserved exons
Gene identifier human	Position mouse	Position human
13350	2	1
13350	3	2
13350	4	3
13350	6	4
13350	7	5
13350	8	6
13350	9	7
13350	10	8
13350	11	9
13350	12	10
13350	13	11
13350	15	12
13350	16	13
13350	17	14

Report
Exon	Number of supporting transcripts
Transcription initiation & first exon(s)
1	1
2	4
Transcription termination & last exon(s)
1	1
5	1
18	3
Exon skipping
5	6
14	5
Intron retentions
9	1
10	1
11	1

Splicing factors
Splicing factor	Exon array	CLIP data	Exon position
CELF1 (CUG-BP)
DAZAP1
ELAVL1 (HuR)
ESRP1/2	Yes
FUS		Yes
HNRNPA1
HNRNPA2B1
HNRNPAB
HNRNPC
HNRNPF-H
HNRNPL	Yes
HNRNPL_2
HNRNPM
HNRNPU
MBNL3KO/MBNL3WT/MBNL3C2C12		Yes
Nova/Nova1		Yes
PTBP1/2	Yes
QKI
RBFOX2
RBM4	Yes
SFRS3 (SRP20)
SFRS6 (SRP55)
SFRS7 (9G8)
SRSF1		Yes
SRSF2		Yes
SRSF5 (SRP40)
TIA1/TIAL1
TRA2A
TRA2B
YBX1

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

	Exon-Intron
Position	Type	Gene coordinates	Chromosomal coordinates	Length	Sequence	Features
1	Exon	1 - 244	107852467 - 107852710	244	sequence	download
1	Intron	245 - 907	107852711 - 107853373	663	sequence	-
2	Exon	908 - 1037	107853374 - 107853503	130	sequence	download
2	Intron	1038 - 5729	107853504 - 107858195	4692	sequence	-
3	Exon	5730 - 5787	107858196 - 107858253	58	sequence	download
3	Intron	5788 - 6210	107858254 - 107858676	423	sequence	-
4	Exon	6211 - 6294	107858677 - 107858760	84	sequence	download
4	Intron	6295 - 6751	107858761 - 107859217	457	sequence	-
5	Exon	6752 - 8352	107859218 - 107860818	1601	sequence	download
5	Intron	8353 - 8680	107860819 - 107861146	328	sequence	-
6	Exon	8681 - 8720	107861147 - 107861186	40	sequence	download
6	Intron	8721 - 9303	107861187 - 107861769	583	sequence	-
7	Exon	9304 - 9431	107861770 - 107861897	128	sequence	download
7	Intron	9432 - 10842	107861898 - 107863308	1411	sequence	-
8	Exon	10843 - 10937	107863309 - 107863403	95	sequence	download
8	Intron	10938 - 11406	107863404 - 107863872	469	sequence	-
9	Exon	11407 - 11520	107863873 - 107863986	114	sequence	download
9	Intron	11521 - 12118	107863987 - 107864584	598	sequence	-
10	Exon	12119 - 12206	107864585 - 107864672	88	sequence	download
10	Intron	12207 - 12695	107864673 - 107865161	489	sequence	-
11	Exon	12696 - 12785	107865162 - 107865251	90	sequence	download
11	Intron	12786 - 13193	107865252 - 107865659	408	sequence	-
12	Exon	13194 - 13282	107865660 - 107865748	89	sequence	download
12	Intron	13283 - 18458	107865749 - 107870924	5176	sequence	-
13	Exon	18459 - 18614	107870925 - 107871080	156	sequence	download
13	Intron	18615 - 19572	107871081 - 107872038	958	sequence	-
14	Exon	19573 - 19639	107872039 - 107872105	67	sequence	download
14	Intron	19640 - 19868	107872106 - 107872334	229	sequence	-
15	Exon	19869 - 19917	107872335 - 107872383	49	sequence	download
15	Intron	19918 - 20333	107872384 - 107872799	416	sequence	-
16	Exon	20334 - 20483	107872800 - 107872949	150	sequence	download
16	Intron	20484 - 20572	107872950 - 107873038	89	sequence	-
17	Exon	20573 - 20623	107873039 - 107873089	51	sequence	download
17	Intron	20624 - 20838	107873090 - 107873304	215	sequence	-
18	Exon	20839 - 22133	107873305 - 107874599	1295	sequence	download

	5' untranslated regions
	UTR 1	UTR 2	UTR 3	UTR 4	UTR 5	UTR 6	UTR 7
Supporting GenBank accession identifers	U77844	AK012948	BC006929	NM_011634	AK040001	AK012786	BC017374
Length	112	111	276	112	108	94	98
Number of ATGs in frame	0	0	1	0	0	0	0
Total number of ATGs	0	0	4	0	0	0	0
Number of GTGs in frame	4	4	3	4	4	4	4
Total number of GTGs	6	6	10	6	6	6	6
Number of CTGs in frame	1	1	0	1	1	1	0
Total number of CTGs	4	4	1	4	4	2	1
Number of micro ORFs in frame	0	0	0	0	0	0	0
Total number of micro ORFs	0	0	2	0	0	0	0
GC percentage	62	61	44	62	62	61	64
Number of pyrimidine tracks	0	0	0	0	0	0	0

	3' untranslated regions
	UTR 1	UTR 2	UTR 3
Supporting GenBank accession identifers	AK040001	BC006929 U77844 BC017374 AK012786	AK012948 NM_011634
Length	1568	2731	1172
Number of ATGs in frame	10	14	6
Total number of ATGs	25	44	19
Number of GTGs in frame	17	25	14
Total number of GTGs	50	95	38
Number of CTGs in frame	13	17	10
Total number of CTGs	29	57	21
GC percentage	49	53	49
Number of pyrimidine tracks	11	21	7

	miRNAs
Identifier	Name	Gene coordinates	Chromosomal coordinates	Prediction algorithm
Group 1
M1	mmu-miR-370	21138 - 21145	107873604 - 107873611	targetscan
M2	mmu-miR-504	21204 - 21225	107873670 - 107873691	miranda
M3	mmu-miR-504	21218 - 21226	107873684 - 107873692	targetscan

	Protein features
Category	Feature identifier	Feature name	Exons	Start on gene	End on gene
No data