Sequence
atgc intronic sequence ATGC exonic sequence...atttaaaaatctttaaagatagagtacatgaaaattaaattcattttacaatgcttactctcgggcacattttcttacaatattcactttatttatatagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC
Basic information
species | Glycine max |
transcript | GLYMA16G22830.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G22830.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g14150.6 (Oryza sativa), 3'ss of exon 3
atttaaaaatctttaaagatagagtacatgaaaattaaattcattttacaatgcttactctcgggcacattttcttacaatattcactttatttatatagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC
||| | | | | | ||| |||| | | || || | ||| |||| | || | || ||||| |||| |||||||| |||||||| ||||| ||||| |||||||| |||||||||||| ||||||| || |||||||||| || |||| ||| ||
--------gtctgcacccgtcaattttcctacgcataacctcatcacaaatatctgac-----gattttatttaacacaactgctaattcttcactacagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCCATTGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTTTACCAGAAGGCCA
upper sequence: GLYMA16G22830.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
atttaaaaatctttaaagatagagtacatgaaaattaaattcattttacaatgcttactctcgggcacattttcttacaatattcactttatttatatagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC
| ||| | | || |||| | | || | | | | || | | | |||| | || ||||| |||| |||||||| |||||||| ||||| ||||| ||||||||||||||||||||| | ||||| ||| | || |||| | ||||| ||| ||
--------------gttagttccttaccttattat--ggttcacctggaagaatgtagcttttg-cttaattaacaatatttttcaatgctgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
upper sequence: GLYMA16G22830.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G008216_T04 (Zea mays), 3'ss of exon 2
atttaaaaatctttaaagatagagtacatgaaaattaaattcattttacaatgcttactctcgg-gcacattttcttacaatattcactttatttata-tagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC----------------------------------------------------------------
|| | ||||| | | || |||| | ||| || ||| || | || ||| | || ||| || | ||||| |||||||||| || |||||||||||||| || || |||||||| |||||||||||| ||||||| || |||||||||| ||||||| ||| ||
gttcgta---ctttactgttctgactgattgc--ctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagaggctggtttatggggccaaggcagaggctgccatcgccattggatttgatgacttcattgcagATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCAACTTGGAGATCAAGAAAGCTGACGGCAATGGTGCATTGATCGCTGAGCAAGTCTTTGAAAAGAC
upper sequence: GLYMA16G22830.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
atttaaaaatctttaaagatagagtacatgaaaattaaattcattttacaatgcttactctcgg-gcacattttcttacaatattcactttatttata-tagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC
|| | ||||| | | || |||| | ||| || ||| || | || ||| | || ||| || | ||||| |||||||||| || |||||||||||||| || || |||||||| |||||||||||| ||||||| || |||||||||| ||||||| ||| ||
gttcgta---ctttactgttctgactgattgc--ctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
upper sequence: GLYMA16G22830.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G050405_T01 (Zea mays), 3'ss of exon 3
atttaaaaatctttaaagatagagtacatgaaaat-taaattcattttacaatgcttactctcgggcacattttcttacaatattcactttatttatatagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC
|| | | | | | | | | | || || || | ||| | | | | |||| ||| | | | || ||||| |||||||||| || |||| |||| |||| ||||| ||||||||||||||||||||| ||||||| || |||||| ||| ||||||| ||| |
gttcataccccactgtt--ttggttgcctaaactcataggcacaactagaaattatcgaatcatgtctaactttcctac------ctgtcttgcaatgcagAGGCTGGTTTATGGGGCCAAGGTAGAGTCTGCCATTGCCATTGGATTCGATGACTTCATTGCAGATGCTCTGAGAGGCATTGGGTTCTACCAGAAGGATA
upper sequence: GLYMA16G22830.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 4
atttaaaaatctttaaagatagagtacatgaaaattaaattcattttacaatgcttactctcgggcacattttcttacaatattcactttatttatatagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC
|| | | || || | | | || || | | || || | | | || | | | |||| || || | ||||| |||| |||||||| |||||||| ||||||||||| |||||||| ||||| |||||| | ||||| | |||| ||||| | ||| | ||| ||
----gttgatttcttaacttacatattcttcatat--gatagaatatatggagcatgttactgatagcaatcttgttcaatg----ctgtact---gcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCAATTGCCATTGGATTTGATGATTTCATTGCTGATGCTCTCAGAGGAACTGGGTACTATCAGAAGGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacaatgcttactctcgggcacattttcttacaatattcactttatttatatagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC
ttcttac putative branch site (score: 2)
ctttattt putative PPT
attttcttacaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttaaaaatctttaaagatagagtacatgaaaattaaattcattttacaatgcttactctcgggcacattttcttacaatattcactttatttatatagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - catgaaa