Sequence
atgc intronic sequence ATGC exonic sequencegttagcatctacataacagcgaaatacacaagtatcatttggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaagGAATTAGACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT
Basic information
species | Glycine max |
transcript | GLYMA13G19500.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 7
----gttagcatctacataacagcgaaatacacaagtatcatt-tggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaagGAATT-AGACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT
| | | | | | || || | || | | || | | | || ||| |||| || ||| |||||||||||||||||||||||| ||||| || || ||||| || ||||| ||||| ||||| || || ||||| |||||
acacaccaacttaaatactcttgggagtcccaggatcatgctaatttcaaaacacttgtcacctcttagaccgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT
upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 7
-----------gttag---catctacataacagcgaaatacacaagtatcatttggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaagGAATT-AGACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT
|| || | || | | | || | | | | ||| | ||| | || || || ||| |||| || ||| |||||||||||||||||||||||| ||||| ||||| |||||||| || || || || |||||||| || |||| || ||
gagaaaaacctgtcaggtgtttttaactctcttaagacggtgtaaatgttagtgcttgcctcctgttagattgaa---------tggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTGAATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT
upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------------------------------gttagcatctacataacagcgaaatacacaagtatcattt--ggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaagGAATTAGACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT
|| || | || | || ||| || | | | | ||| || | | | | |||| ||||||||| ||| ||||||||| ||||||||||||||||||||||| ||||||||||| || | || ||| ||||| || ||| ||||||||||
gtatccttctaaaaattcttaatccttagcaaacactagtttaaaacgattcttcaagcatactgtccttaaaatacttgtttatttttttataatctcaaatctagaaaattggatctaaatcatccttt-ttttccttaataaaccaatcagACAAGAAAAATGAGAACAAGGAAGTTGCAGTTAACGACTTTCTGCCATCTTCCAGTGCTTATGAGGCAATCCAGCATTCCAT
upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------gttagcatctacataacagcgaaatacacaagtatcatt---tggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaagGAATTAGACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT
| | | | | || | | | || || || || | | ||| | | | | | || |||| ||||||||||||||||||||||||||| | ||| | |||| || | |||||| | |||| |||| || |||||
gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagggaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggtttgg--ggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT
upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------gttagcatctacataacagcgaaatacacaagtatcatt---tggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaagGAATTAGACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT
| | | | | || | | | | || || || || | | ||| | | | | | || |||| ||||||||||||||||||||||||||| | ||| | |||| || | |||||| | |||| |||| || |||||
gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagagaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggtttgg--ggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatttggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaagGAATTAGACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT
tcttaat putative branch site (score: 3)
tttttgtgtttttctt CT-rich tract
taaaatcaaactattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcatctacataacagcgaaatacacaagtatcatttggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaagGAATTAGACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC