Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
Basic information
species | Glycine max |
transcript | GLYMA02G43540.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
|| | | | | | ||| || || ||| |||| | | || || || || | || |||||| | || | | ||| ||||| | ||||| |||||||| ||||||||| | ||||||||||| || ||||| ||||||| ||||| ||||| |||||||| || ||||| || |||
---------------------------------------gtatttcttgctctgttccacagttcattttgcac-acttgtgttat--tttctgaacttggattcatgatatttatgtat---------tcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G126795_T01 (Zea mays), 3'ss of exon 9
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgc-ttgcttaagttttctacagattatttacgcatggctatcat---tttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
| | || || | || ||| || ||| | ||||| | | | | || | | | ||| | | | || || ||||| | |||||||||||||||||||| || | ||||||||||| || ||||| ||||||| || || ||||| |||||||| || || || || |||
---------------------------------------------------gtatccactctattttacagttcattctgcaatggccattgctgtattataattcaaactgag-gcatgtggtttttgtgtattgtgacatgctagAGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
||||| ||| | ||| || || || || ||| ||| || | | || || ||| | | || | || ||||| | |||||||||||||||||||| ||| | ||||||||||| || ||||| | ||||| | || ||||| |||||||| || ||||| || |||
----------------------------------gtatccactctcta------ttcgacagttcattctgcaatggctgtattgtaattc----aaactgaggcatatggtttctgtgta--------ttgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
| || |||| | | | | ||| || | || || | | | || | | |||| ||| ||||| | | || | |||| |||||||| | ||||| ||||||||||| ||||| ||||| |||||||| ||||||||| ||||||| || || ||||||||||||||||| || ||||| |||
------------------------------------gtgagtacttt----acccaaagtatctaacatcgcacctataag-atattcat-ctcatgaattctgcagcgtatttg-----aatttttatgtaaactgaggcagAGTCTTATGGAGTATGAAGAGCACGAAAAACGTGCCTGGAGTGTTGACTTTTCACGAACAGAACCATCAATGCTTGTATCTGGTAGTGACGACTGCAAG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttctt-gtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
|| ||| | || | | || || || || | | || | |||| ||| |||| || | | || | || || || ||| ||| | | ||| |||||| | ||||||||||||||||||||||| || ||||||||||| || |||||| | ||||| ||||| | |||||||||||| || ||||| ||||||
---------------------------ggtcctttgaatgaaaaattctgggctcgccactgacta--------tagatt----tgtccttgtata---tatatatatat-atatatatatg-ctaataaatgttttttatcagAGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgct-taagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
|| | ||| ||| | | ||| || | | ||| | | || || | || ||| | || ||| | ||| | | | | | || | | | ||| || ||| ||||| | ||||||||||| |||||||||||| | || |||||||| || |||||| |||| ||||| | ||||| || || || || ||||| | |||
gtctgtccctcattttgatga-cgttaagttgaagttaccaccccttgaat-tatttttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaattt-tttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S180_148V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
|| |||| ||| || | | || ||| | | || | || || ||| ||| || |||| | | | | | ||| | ||||||| | ||||||||||| || |||||||||||||| ||||| | || ||||| | |||||||| || ||||| || ||||| || || || | |||
----------------------------------atacaagatgagggggagcaatcctagagaaaaattagtacgtgagtaaggt--ttacttgtgttacttat--gttatcttcctaag-----taatttgtttcgtgcagAGTGTGATGGAATATGAGGAACATGAAAAGCGTGCTTGGAGCATCGATTTTTCTCGTACAGATCCATCAATGCTGGTTTCTGGAAGTGACGATGGAAAG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
---------------gtaaatgttgaattcaaatggtcagtttgttcttgta---tcagatctttgggtatctt---cattcatta-atattgttttgattgtcatgtgcttgcttaa-gttttctacagatt-atttacgcatggctatcattttaactttg--------gcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
| ||| ||| ||| | ||| | |||| || | |||| |||| || | ||| | | ||||| | | || | | || | | | | || | | ||| | | ||| || | | | |||||| ||| ||| |||||||||||||||||| | ||||||||||| || |||||| |||| |||||| ||||| | || || || |||||||| | |||
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggca-agttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
ttttaac putative branch site (score: 2)
tatcattttaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC