Sequence
atgc intronic sequence ATGC exonic sequencegtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
Basic information
species | Glycine max |
transcript | GLYMA12G29120.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtgga-acatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttca-acccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
|| || | || |||| | | | ||| | || || | || ||||| | | | || || | |||||||||||||| |||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||||||||||| | |||||||||| |||||||| |
-----------------------------------------------------gtgattgactatctatattcaaataatgtacaaattctgttatgcgcttcat-acatcctcttgctgacatttttattcaatatcagGAAAGAGATGTCAGTGAAGAATCTGGATGGAAGCTTGTCCATGGGGATGTTTTCCGGCCTCCTCGCAGTTTGGCTCTTCTTTCAGCCCTTGTTGGTGTTG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
|| ||| | ||||| || ||| || | | ||| | ||| | || || | | ||| |||| || | | || | || |||||||||||||||||||| |||||||| ||||| ||||| ||||| |||||||| ||||||||||| || ||||| ||||||| ||| ||||||||| |
------------------------gtgactggacgaattatttg--aatattcata-gcaaatcattttgcattattttcatctaatctcttgatagtt----ttgttaacttatatttttcttttat-------cagGAAAGAGATGTTAGTGAGGAATCTGGTTGGAAGCTTGTCCATGGAGATGTTTTCCGGCCTCCTCGTAGCTTGGTGTTTCTTTCTGCTTTTGTTGGTATTG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
|| | ||| | | | | | | || | | | || | | || | |||| | |||| | || | | || || |||| ||||| | || || |||| |||||||||| ||| |||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||||||| ||||||| || ||||||| | |
----------------gtatatctaccttttgtttaattgtattcttagctcta-gcatctaagttggatt-tgttttcacctagtgc-cact-cgattgggacc-tcaagtcttgatattcctt------ttgttagGAGAGAGATGTTAATGAGGAATCTGGATGGAAGCTTGTTCATGGTGATGTATTTCGCCCTCCTCGAAGTTTGGCCTTTCTTTCTGCAGTTGTTGGCATCG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 6
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
||||| | | | || | || | |||| |||||| ||||||| || |||| ||| | | || || | || ||| || || | ||| ||||| ||||||| | |||||||||||| ||||| ||||| |||||||||||||| ||||||||| ||| | | ||| ||||||||||| ||||||||| |
gtgagtttctatatatatgatcatggtgttattccagtagcgttttaatatttatgc---------aggttctgattt--taattagtttatacttgtatcctttgctgatatacattagtt-----tgtatt---agGAACGAGATGTCAATGAAGAATCTGGATGGAAGCTTGTACATGGTGATGTTTTCCGGCCTCCTTGCAATCTAGTTCTTCTTTCAGCTCTTGTTGGTATTG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
| || | | | || || || || | | | | | || | | || || ||| || | || || | | ||| ||||| ||||||||| ||||||||| || ||||| ||||| ||||||||||| || ||||||||||| | ||| ||||||| || | ||||||| |
------------------------------aataaaattgaatcatacaagttccaagtaaca-acaagtaacaagtttttctttgactcgatg-------gatcgtttaggattaagatacagttttcctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTGTTCCGGCCTCCTCGTGGCCAGGTGTTTCTTTCTGCCCTAGTTGGTATTG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaaccccca----tacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
||| | | | || ||| | ||||| | |||| || | |||| ||| | | | || || | | | || ||| ||| | || ||| |||| |||| |||||||||| ||| ||||| || ||||| ||||| |||||||| || ||||||||||| || |||||| | ||||||| || ||||||||| |
-----------gtgagga--gctgaattctggcgcgcctactgtttaac-tgtatgcttgatagctagagaaatgttttcactagattttgctg-gctccccccactccattgttgcttaagttatgatattacctttctagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGTGACGTATTTCGGCCTCCCCGAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
| || |||| | ||| | | | | | | | ||| |||| | || | | || || | || | | | ||| ||| |||| |||||||||| ||| ||||| || ||||| ||||| ||||| ||||| ||||||||||| | |||||| | ||||||| || ||||||||| |
-----------------------------------aaacatgccttaatagtta-gagaaacattttcactagattttgctggcttctgcactccattgttgctta--agttatgatatattgatattacctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactatt------attactatttt-----ttaaaatttatgtgtggaacata-gattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
|||| | || || | ||| | ||| | || | ||| | |||| |||| | | | | | | || ||||| | | || | | || | || |||| | | |||||| | ||||| |||||||||||||| ||||||||||||||||| ||||| || |||| | | ||| | ||| | || ||||| | ||||||||||
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattg-atgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
|| || | ||| || |||| | | | | | | | | || ||| | | |||| || | ||||| | | || ||| | ||| |||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||||| |||||||||| || ||| ||| | ||||||||| ||||||| ||||
------------------------gtgacactctcaacttttgtttatattctttttcctttaattgg--------tttgtgggatttccatttc--ttttaattgtaa---ccattttaacatgta---attctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttc--tgattgtcaattcttgt-tcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
|| | | ||| || || || || | | || | ||| | || || || || || ||| | | | | | | || | ||| ||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||||||| ||||||||| | ||||| | |||||||| ||||||| || |
----------------------------------gtaatgctattttaagttcttgactgtgtctatgtttttttttttttttaatatatatagtccttaagtgaaaattatgtatcttattttccactatatattgtcagGAAAGGGATGTAAGTGAAGAGTCTGGCTGGAAACTTGTCCATGGGGATGTTTTTCGGTCTCCTCGCAATATGGTTTTATTTTCAGCTGTTGTTGGCACTG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
| | || ||| | | || | || | || |||||||||||| || || |||||||| ||||| ||||| ||||| || |||||||| || | || || ||| | | ||| | || || | |||||||||| |
--------------------------------------------------------------------------------------gtacgtttatgttgcgcattgcagtggctgaaaga-------acttttccagGAAAGGGACGTGAGTGAAGAGTCTGGATGGAAGCTTGTCCACGGTGATGTCTTCAGACCGCCACGCTATCTTGTTTTGCTGTCTTCGCTTGTTGGTACCG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 7
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
| | || ||| | | || | ||| | || |||||||||||| || || |||||||| ||||| ||||| ||||| || |||||||| || | || || ||| | | ||| | || || | |||||||||| |
--------------------------------------------------------------------------------------gtacgtttatgttgcgcattgcagtgtttgaaaga-------acttttccagGAAAGGGACGTGAGTGAAGAGTCTGGATGGAAGCTTGTCCACGGTGATGTCTTCAGACCGCCACGCTATCTTGTTTTGCTGTCTTCGCTTGTTGGTACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
ttctgat putative branch site (score: 3)
catttcc putative PPT
atacattt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT