Sequence
atgc intronic sequence ATGC exonic sequence...attttattaaaaaaggtgttttttttatataaaaaaatgagcttaaacaaatgggccaactatgataaagtattcttgagaaaattgtctctctttgcagAAATTTTTGAATTTGATGCAATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATAAAGCTGCATCTCTGGGACG
Basic information
species | Glycine max |
transcript | GLYMA07G39920.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G39920.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 3
attttattaaaaaaggtgttttttttatataaaaaaatgagcttaaacaaatgggccaactatgataaagtattcttgagaaaattgtctct--ctttgcagAAATTTTTGAATTTGATGCAATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATAAAGCTGCATCTCTGGGACG
||||| | || |||| | | || | | || || || || | ||| | | | || |||| |||||||||||||||||||||||||| ||||| || ||||| || || || | | | || || |||||||||||||| | |||| ||| || ||||| || |
--------gtaaaagtttggcttattatcttatgttataattgctgctatataa---aattacaattcataattttgcaacatatcttctcaaaatttgcagAAATTTTTGAATTTGATGCCATGGAAGATCCTCCATCCGTTATGAAAATAAATGTCTACGATTTTGATGGACCATTTGATGAAGTTGAGTCTCTTGGTCA
upper sequence: GLYMA07G39920.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g38440.1 (Oryza sativa), 3'ss of exon 3
-----------------------------attttattaaaaaaggtgttttttttatataaaaaaatgagcttaaacaaatgggccaactatgata-aagtattcttg------------agaaaattgtctct---ctttgcagAAATTTTTGAATTTGATGCAATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATAAAGCTGCATCTCTGGGACG
|| || | | | | | ||| | || | || | | | | | |||| | || ||| || | ||| |||| || ||||||| || |||||||||||||| |||||||| || || || ||| || |||| | || ||||||||||||||||| | ||| ||| | | || || ||||
gtatgtgtttggcattacagttcaaattttttcccttttagatgtttccctctttttttaggtatataactacatgtactggattttattatggaacaaaggttcatggcacaagcaactaaaaatttgttcctaaatattgcagACATCTTTGAATTTGATGCCATGGATGATCCACCATCAGTGATGAATGTACATGTATATGATTTTGATGGACCATTTGACGAAGTTACCTCACTTGGACA
upper sequence: GLYMA07G39920.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G179351_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------attttatta--aaaaaggtgttttttt----tatataaaaaaatgagcttaaacaaatgg-gccaactatgataaagtattcttgag--aaaattgtctctctttgcagAAATTTTTGAATTTGATGCAATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATAAAGCTGCATCTCTGGGACG
|| || | | || ||| ||| | | ||| | | | ||| | | | | || | | | | | | |||||||||| ||||||||||| ||||||||||| || || || ||| || ||| | || ||||||||||||||||| | ||| ||| | |||| || ||||
gtatacattttctgcgactgtttctggcttcttcttaaaccttgtcatctgcttccatcactaggaaattgtaaatttgaactgcaccaaattttagtagcatagaaacagtgtgttttgttatgccatgcaactaaacctagttcaccaaatcttgcagAAATCTTTGAATTTGACGCAATGGATGATCCACCGTCGGTGATGAGTGTACATGTATATGATTTTGATGGACCATTCGATGAAGTTACATCCCTTGGACA
upper sequence: GLYMA07G39920.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------attttattaaaaaaggtgttttttttatataaaaaaatgagcttaaacaaatgggccaactatgataaagtattcttgagaaaattgtctctctt-tgcagAAATTTTTGAATTTGATGCAATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATAAAGCTGCATCTCTGGGACG
| |||| || |||| | | | | |||| ||||| | || || ||||| | | || ||||||||| |||||||| |||||||||| ||| ||||||||||| ||| |||| ||||||| |||||| |||||||| | ||| | |||| || |||| |
gtaaatggttactctatggtttttatgtctagttatcttagtggtagcatggtcttatcctcaagctgacttttcatccacttgttttcgtcaattcttgaatgtttcaactctt----tgtttttttgagggtggaattttgtttgtgcagAAATATTTGAATTCGATGCAATGGCTGATCCTCCTTCTGTACTGAATGTTGAAGTTTTTGATTTCGATGGACCTTTTGACGAGGCTGTTTCATTGGGGCA
upper sequence: GLYMA07G39920.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------------attttattaaaaaaggtgttttttttatataaaaaaatg-agcttaaacaaatgg-gccaactatgataaagta---ttcttgagaaaattgtctctc-tttgcagAAATTTTTGAATTTGATGCAATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATAAAGCTGCATCTCTGGGACG
||| ||| || || | | | | | | ||| | | |||| ||| || | | | | || | | | || ||| || |||| ||||||| || ||||||||||||||||||||||| ||||| ||| |||||||||||||||||| |||||||||||||| | |||| ||||| |||| ||||| |
gtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgtcttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaaatgggccaactatgataaagtattcttgagaaaattgtctctctttgcagAAATTTTTGAATTTGATGCAATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATAAAGCTGCATCTCTGGGACG
ttgtctctctttgc CT-rich tract
tatgataaagtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttattaaaaaaggtgttttttttatataaaaaaatgagcttaaacaaatgggccaactatgataaagtattcttgagaaaattgtctctctttgcagAAATTTTTGAATTTGATGCAATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATAAAGCTGCATCTCTGGGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - -taaaaaa
- - - - - - - ggtgttt
- - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacta