Sequence
atgc intronic sequence ATGC exonic sequence...agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttctttaattcaacattcacatacttatattttgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
Basic information
species | Glycine max |
transcript | GLYMA02G42560.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 23
---agtacact-ccgtcactttagaggagctctatttgtggtcctt--aatccaccaaatcaattttctttaattcaacattcacatacttatattttgat-gacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
| | | | | | | | | | || || | | ||| | | ||||| || | || ||| | | || | | | |||| || | ||| ||||| ||||| ||||||||||||||| |||||| ||||||||| | ||||| |||||||||||||||||||| ||||| || || || ||||| |||
gtatgcaaattgtttttattcttcataccttttaattttatttcttctgaatctttaaatccatcta--ttgatt--gcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23
agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaatt--ttctttaattcaacattcacatacttat--attttgat-gacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
| | ||| | || || | | | || | |||| | | | | ||| | | ||||| || |||| || | ||| ||||| ||||| ||||||||||||||| |||||| ||||||||| | ||||| |||||||||||||||||||| ||||| || || || ||||| |||
---gtatgcaaattgtttttattcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 21
-------agtacactccgtcacttta--gaggagctctatttgt---ggtccttaatccaccaaatcaattttctttaattcaacattcacatacttatattttgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
| || | || ||| || | | | ||||| ||||| || | | | || | ||| || | | ||| | ||| ||||||||| ||||||||||||||||||||| |||||| |||||||||| | ||||| |||||||||||||||||||| ||||| || || || || || ||
gtatataattatttttgttcctgttactgatgccttttgtttgttccagtcctctatatattgagcaatggctcgcttggtcatgtcacataaatttaaaattt-----cagATATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACCGCA
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 12
---agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttct--ttaattcaacattcacat-acttatattttga-tgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
||| | | | | | | | || | | || ||| ||||||| ||| | || | |||| || | | ||||| | |||||| ||||| ||||||||||||||||||||| |||||| |||||||||| | || || |||||||||||||||||||| ||||| || || || || |||||
gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgt-ccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
---agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttct--ttaattcaacattcacat-acttatattttga-tgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
||| | | | | | | | || | | || ||| ||||||| ||| | || | |||| || | | ||||| | |||||| ||||| ||||||||||||||||||||| | |||| |||||||||| | || || |||||||||||||||||||| ||||| || || || || |||||
gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgt-ccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 23
agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttctttaattcaacattcacatacttatattttgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
| | | | | | || | || | || ||||| | | || || | | || | |||| || || | ||| || || || ||||| ||||||||||| | |||| || |||||| || ||||||||||| ||||||||||| || || ||||| |||||||||
---gtatttgattattgcttactag----acttcttacttatattccac---actagttactttgtagactacttacacacg---attttccaactgcagGTACGTAGTGGAGAGGATGGATGGTGACCTCTGGGAGAAGGTTCTTACGGAAGAAAATGAATATAGGAGGCAACTTATAGACCAAGTTGTGTCTACTGCT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttctttaattcaacattcacatacttatattttgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
| | ||| | | || ||| || | || ||| | | ||| | | || || | | || | ||| || || ||||| || ||||| |||||||||||| |||||| ||| ||||| ||| | ||||| |||||||| || |||||||| || ||||| |||||||||
---gtattttatcattacttacgaa---aattcttgttactc---tcacaatggtgactttgt--agtttg---ttaatacacaagt-tttcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 23
agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttctttaattcaacattcacatacttatattttgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
| || |||| | | || | | || | || || | ||| || || | || | || ||| ||| || || ||||||||| ||||| || |||||| |||| | |||| ||||||||||| ||||||||||| |||||||| || || |||||||| || ||||||||||||
------gtttgtgacttgtttacttcccgatatattatcat--atgcatggattca---tttggtacatggacgct-acttacacatacttccatttcagATATGTAGTTGAAAGGATGGATTCTGATCTCTGGGAGAAAGTTCTTGACCCTGATAATGATTATAGAAGACAGCTCATTGATCAAGTAGTATCTACTGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaccaaatcaattttctttaattcaacattcacatacttatattttgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
ttttgat putative branch site (score: 4)
aaatcaattttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttctttaattcaacattcacatacttatattttgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
- tacactc
- - - - - - - - - - - - - - - - - - - - - - - caccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatac