Sequence
atgc intronic sequence ATGC exonic sequencegtcttgtattttaaaaaattaattgtgattaaatatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
Basic information
species | Glycine max |
transcript | GLYMA04G09070.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 14
-----------------------------gtcttgtatt--ttaaaaaattaattgtgattaaatatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
||| ||| || | | || | | | |||| | | |||| || | ||||| | | |||| | | || | |||| || |||||||||||||| ||||| |||||||| || |||| | | |||||||||||||||||||| || |||| || || ||||| ||||| | |
gtacgtttggagtgtccaagagccttgtaaaattgaattcattttagcagcaagctacactgactatcaattgaatatgtaaaagtct-tgagattt-tattatctcgcatatctcttttgtagGTAGTAGAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGGGATAGTGGTTATCGCATAACTGCAACAGCAGCCACATGTGACCAGGTGG
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 14
-----------------------------gtcttgtatt--ttaaaaaattaattgtgattaaatatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG----
||| ||| || | | || | | | |||| | | |||| || | ||||| | | |||| | | || | |||| || |||||||||||||| ||||| |||||||| || |||| | | |||||||||||||||||||| || |||| || || ||||| ||||| | |
gtacgtttggagtgtccaagagccttgtaaaattgaattcattttagcagcaagctacactgactatcaattgaatatgtaaaagtct-tgagattt-tattatctcgcatatctcttttgtaggtagTAGAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGGGATAGTGGTTATCGCATAACTGCAACAGCAGCCACATGTGACCAGGTGGCTTT
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 14
---------------------------------------------------------------------------------gtcttgtattttaaaaaattaattgtgattaaa-tatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
| || | | || || || | | ||| || || | | | | || || | |||| | || | |||||||||| ||||| ||||||||||| ||||| ||||| |||||| | ||||||| ||| | ||||||||| | ||||| || |||||||| || || |
gtacgttgacgtgctcagaaggctggcctttgctttgaatcgtctactatccaggaaaaaacatatcgacatgccttgatattgctgactctcaagaacatagcttcaagaaaaacatatgctgaaaacagcattgttaaacttggttct-tatttttaatgtttttggttttagGTTGTGGAGCTTGACTTCTTGTATCCAAGTGAGGGTATCCATCGACGATGGGATAATGGATTTCGCATCACGGCTACTGCAGCTACATGGGATCAGGCAG
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G095634_T01 (Zea mays), 3'ss of exon 7
--gtcttgtattttaaaaaattaattgtgattaaatatc----cttgtggc---actgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
||| | | | | | | | | || | || || || || ||| |||| | | || || | | | || | | |||||| || ||||| ||||||||||||||||| || || |||||| ||||||||| || ||||| | || ||| || || |||| || || || || ||||
gagtcgttcagatcgacta-tcacctctgcaccgacttctcgactagtcgcccgactttaaaacctcgtttcttattgaactattggcat-ttactttccagGTGGTTGAACTGGATTTCTTGTATCCCAGCGAGGGAATTCATAAAAGGTGGGACAGGGGTTACTGGATAACCGCAGCTCCTGCTACTTGTGATCAGGCTG
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 14
-------------------------------------------------------------------------gtcttgtattttaaaaaattaattg--tgattaaatatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaat-gcc------agGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
| ||| | |||| ||| || ||| | || | ||| | | | | || ||| || || || | ||| |||| || || ||||||||||||||||||||||||||||||||| || | ||||| ||||| || ||||| ||||| |||||||| || ||||| || || |
gtaattagcgctctaagcctacttgatttacgaaaaccgcatactatttttgcttcttcgactcggagcagatatgaagtaaatgaaaatatttgctgaccaatttagaattcctgtcatcggacatcacctgattacattcctctctcttaccgaatgtatttgccctctgcagGTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGGGACAGTGGATACCGCATAACCTCTACTGCTGCGACTTGGGATCAGGCAG
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
---------------------------------------------------------------------------------gtcttgtattttaaaaa---attaa-----ttgtgattaaatatcct--------tgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgcc---agGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
|| | || | | | || | |||||| || | | | ||| ||| | | || || || | | | || | |||| || || ||||| ||||||||||| || ||||||||||| | | ||||| ||||| ||||||||||| || |||||||| |||||||| ||||| |
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 12
gtcttgtattttaaaaaattaattgtgattaaatatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
| | |||| | || | | | | ||| ||| | | || |||| ||||| || |||||| | |||||||| ||||| || || || |||||||| |||| |||||||||||| | ||||| ||||| ||||| ||||| |
--------------------------gtctgttaatccattcgggcttcgcacacttgtttgacagcgctatatgcattacac--------agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
gtcttgtattttaaaaaattaattgtgattaaatatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
|| | | | | | | | || | | | | | | | | | |||| ||||| || |||||| | |||||||| ||||| || || || |||||||| |||| |||||||||||| | ||||| ||||| ||||| ||||| |
----------------------------------gtctgttaatccattcgggcttcg-cacacttgtttgacagcgctatgcatgacac-agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
acttaat putative branch site (score: 4)
atttatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttgtattttaaaaaattaattgtgattaaatatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG