Sequence
atgc intronic sequence ATGC exonic sequence...ttttttccatctctttaattttgcaataatttgtagtaatttttagaacaaccataatgtcattttgttagcttcttatgctattattgtggttgtaaagGTTCTGATGAAGGAATGTATGCTTGGGTTGTTGCTAATTATGCACTTGGCACTCTTGGAGGTGATCCTTTGGAAACTACTGGGATTATTGAACTTGGTGG
Basic information
species | Glycine max |
transcript | GLYMA02G11980.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G11980.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g26080.1 (Oryza sativa), 3'ss of exon 1
ttttttccatctctttaattttgca-ataatttgtagta-atttttagaacaaccataatgtcattttgttagcttcttatgctattattgtggttgt-aaagGTTCTGATGAAGGAATGTATGCTTGGGTTGTTGCTAATTATGCACTTGGCACTCTTGGAGGTGATCCTTTGGAAACTACTGGGATTATTGAACTTGGTGG
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-agggaaaatccattggatggtggatacagatggtttttcatcattagctgaa--atattgtcagtatggatgctcattttttggctggttcatttcttatagGCTCTGATGAGGGTATCTATGCTTGGGTTGCGGCAAACTATGCTCTTGGCACACTTGGAGGGGATCCACACAAAACCATTGGAATAATTGAACTTGGGGG
upper sequence: GLYMA02G11980.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G14230.1 (Arabidopsis thaliana), 3'ss of exon 1
ttttttccatctctttaattttgcaataatttgtagtaatttttagaacaaccataa--tgtcattt-tgttagcttcttatgctattattgtggttgtaaagGTTCTGATGAAGGAATGTATGCTTGGGTTGTTGCTAATTATGCACTTGGCACTCTTGGAGGTGATCCTTTGGAAACTACTGGGATTATTGAACTTGGTGG
||||| || | | | || | | | | |||||| | | | | |||| | | || ||||| | | || | | | | ||| ||||||||||| | ||||||||||||||||||||| |||| || || | ||||||||||| ||||| |||| || || ||| ||||||| |||||
tttttgttatatagt-agcttagt--tgagtgctagtaaaataaatgagatccattggctattgttggtgttataattactagaaatcttggaaaattttcagGATCTGATGAAGGTGTATATGCTTGGGTTGTTGCTAATCATGCGCTCGGTTCGCTTGGAGGTGAACCTTTAAAAACAACGGGAATTGTTGAACTCGGTGG
upper sequence: GLYMA02G11980.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G14250.1 (Arabidopsis thaliana), 3'ss of exon 2
--ttttttccatctctttaattttgcaataatttgtagtaatttttagaacaaccataatgtcattttgttagcttcttatgctattattgtggttgtaaagGTTCTGATGAAGGAATGTATGCTTGGGTTGTTGCTAATTATGCACTTGGCACTCTTGGAGGTGATCCTTTGGAAACTACTGGGATTATTGAACTTGGTGG
| ||| | ||||| | || | | | |||||| | | | | |||| | ||| ||| ||| || | ||| |||||||||| || ||||||||||||||||| ||| | |||||||| | ||||| |||||||| ||| |||| || |||||| |||||||||||||
tttcattttgttttcttttagctta-gttgagtgatagtaaatgtgcacatatccattg-gcaattggaagtgctaattactggggggaaaattttattcagGAACTGATGAAGGTATCTATGCTTGGGTTGTTGCCAATCACGCACTTGGTTCGCTTGGTGGTGATCCATTGAAAACAACGGGGATTGTTGAACTTGGTGG
upper sequence: GLYMA02G11980.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0026g02490.t01 (Vitis vinifera), 3'ss of exon 1
ttttttccatctctttaattttgcaataatttgtagtaatttttagaacaaccataatgtcattttgttagcttcttatgctattattgtggttgt---aaagGTTCTGATGAAGGAATGTATGCTTGGGTTGTTGCTAATTATGCACTTGGCACTCTTGGAGGTGATCCTTTGGAAACTACTGGGATTATTGAACTTGGTGG
|| || ||| ||| ||| | || | | | | ||| || || | ||| | || | || |||| | ||| || ||||||||||| ||||||||||||||||| ||| |||||||||||| |||||||||||||||| |||||| |||||||||||||| ||||||||
------gtattggattgattacattggcattggtaacatttatctctcttgc--ttgtacattttcattgaattttgatggttttcctatgtttgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCAGTCTTGGAGGTGATCCTCGGGAAACAACTGGGATTATTGAGCTTGGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacaaccataatgtcattttgttagcttcttatgctattattgtggttgtaaagGTTCTGATGAAGGAATGTATGCTTGGGTTGTTGCTAATTATGCACTTGGCACTCTTGGAGGTGATCCTTTGGAAACTACTGGGATTATTGAACTTGGTGG
attttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttttccatctctttaattttgcaataatttgtagtaatttttagaacaaccataatgtcattttgttagcttcttatgctattattgtggttgtaaagGTTCTGATGAAGGAATGTATGCTTGGGTTGTTGCTAATTATGCACTTGGCACTCTTGGAGGTGATCCTTTGGAAACTACTGGGATTATTGAACTTGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - ccatctc
- - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - caaccat