Sequence
atgc intronic sequence ATGC exonic sequencegtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
Basic information
species | Glycine max |
transcript | GLYMA03G32620.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 3
gtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
|||| | || ||| | | || || |||| | | | || | | | || | | | ||| | | | || ||||| || | |||| ||| || | |||||| || ||||||||| | ||||| || || ||||||||||| ||||| ||||| |||||||||||||||
---------actattc--ttcattgtctattttaactgttgag------ttacatagttttgtactctcactcttat--acctaacttttccctggaatgaaaccttttctgta-----ta-cagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 2
-----------gtactttcacttattta-gtcca---caagttatatcgaggaaaaagcatgccttttgagaat-ttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
| ||| | |||||| | ||| || |||||||| | || | | | |||| | || | || || |||| || | || |||| ||| || ||| || ||||| || | |||| ||| | |||||| |||||||| ||| | ||||| ||||| ||||| ||||||||||| || || || |||||||| |||
gtaaggaaagccttttttgagatatttaagaccagtccataatatatcgactactgag--tcacatgtgagtctgttcacatctttcttttttttggttggctcg--ttta------aacctcactgggaa-------cagGGCAGAATCACAGTCCCTGCATAGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAA
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G353548_T04 (Zea mays), 3'ss of exon 2
gtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaa----attttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattat---cagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
| || ||| ||| | | ||| || || | | || | | | ||| || | | | ||| | | | | ||||| | || | | | | | | | | | ||||| || | ||| ||| | | |||||| |||||||| ||| | ||||| ||||| ||||| ||||||||||| || || || |||||||| |||
---gtaaggatttttttgtctcaatgatat-tcaagaacagtccacaacatattcactactgagtcgcatgtgagtctgttc--gcatctttatttttattggctgattcgtttaaacctcactgtgtacagGGCAGAATCACTGTCCCTGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAA
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G43930.4 (Arabidopsis thaliana), 3'ss of exon 2
gtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatca-gGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
| | ||| | | | | | |||| || | | |||| | | | | | | | |||| | |||||||||| |||||||||| |||||| ||||| || ||||||||| | ||||||||||||| |||||||| || || ||||| | ||||| | |
--------------------------------------------gtacactttatgtttct----tgtctctttatttgcataggaccttgtttaagctcattgtaattggtgattctttatgaagGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCAAAATATTGTCCTCTTGGAGCTCCTCCAAGGTCAACTATTGCTGCGGCTTTTAGTACTGATGGAAGA
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G04140.2 (Arabidopsis thaliana), 3'ss of exon 2
gtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
||| || | | || | || | ||||| | | ||| | ||| | | | ||| | | ||| ||| || ||| ||||||||||| |||||||||| |||||| |||||||| || |||||| | | |||||||||||||| || ||||||||||| ||||| ||||||| | |
--------gtacctttcgttcgtcacttcttc----------gcttctctttttgatgt---gatccctgcctcctttcgggcatctgaatgtaa---actgcattccctac--atg-----tagGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGA
upper sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
gtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
| || || || | | | |||| | | || | || |||| | || | || || || | || | ||||| ||||| || ||||||| |||||| || || | |||||||||| || |||||||||| ||||||||||||||||||||||| || |||||||| |||
---------------tcgtacaaggtttttgcttctgttttcatacaagttttttgcttctgttttctttcttttt---------atctttctttctttcttttttgttccttttctgttct-agGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
aaaagtcaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG