Sequence
atgc intronic sequence ATGC exonic sequence...atcattcctgagatgctagcagtgatgtggggtgaatgcccaaagtgcctgttaacatagctagccagatctctaacagcttattttgcaatttctgtagATAGGGACATTTAATCATGCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTG
Basic information
species | Glycine max |
transcript | GLYMA09G24430.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G24430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 5
-atcattcctgagatg-ctagcagtgatgtggggtgaatgcccaaagtgcctgtta-acatagctagccagatct--ctaacagcttattttgcaatttctgtagATAGGGACATTTAATCATGCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTG
|||| | || || || | | | | | | | | ||| | | | | ||| || | | | ||| | ||| | | | || || || |||| ||| ||| |||||||||||||||||| |||||||||||||| | ||||| |||||||| | |||| ||||| | | |
tggcattaccgatatctcttgaacttttatttgctca----ccagtttacttttggtgcatgattatgttgttgttgttaatttcctatatactgaata-tgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG
upper sequence: GLYMA09G24430.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G25720.1 (Arabidopsis thaliana), 3'ss of exon 5
--atcatt--cctgagatgctagcagtgatgtggggtgaatgcccaaagtgcctgttaacatagctagccagatctctaacagcttattttgcaatttctgtagATAGGGACATTTAATCATGCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTG
|||| | || | | | | | | | | | | | || || | || | | || | |||| | |||||| || ||||||| ||| |||||||||||| ||||| ||||| || |||||||||| || |||||||||||||| | ||| ||||| |||| || |
ttgtcataggtttaagctacca-tgtttccattgcttcaccactttat-tatggactagtattgttattttcttttatattaagca--tttgatttcactgtagGTAAAACCATTTAAACATCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGG
upper sequence: GLYMA09G24430.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01140.t01 (Vitis vinifera), 3'ss of exon 5
atcattcctgagatgctagcagtgatgtggggtgaatgccc---aaagtgcctgttaacatagctagccagatctctaacagc--ttattttgcaatttc---tgtagATAGGGACATTTAATCATGCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTG
|| |||| || | | || || | ||| | | | | | | | |||||| | | | | || | ||| || || | | |||||||| | || |||| ||||||||||| ||||||||| |||| |||| ||||||||||||||||| | ||| ||| ||||||| ||||
-------ttggtgtgctcttt-tggaataagatgcattctttgtgaagagtccaattagttgcttgccaagatctgttatgacattcatgcttttattctcagtgcagTTTGAGACATTTACTAATCATATGCGGGATGGTTGGGGACTGGCAACTAATGGGGAAGTTTTGTTTGGAAGTGATGGAACTTCGACACTGTATCAGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcctgttaacatagctagccagatctctaacagcttattttgcaatttctgtagATAGGGACATTTAATCATGCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTG
ctctaac putative branch site (score: 2)
tttctgt putative PPT
ttattttgcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcattcctgagatgctagcagtgatgtggggtgaatgcccaaagtgcctgttaacatagctagccagatctctaacagcttattttgcaatttctgtagATAGGGACATTTAATCATGCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- cattcct
- - - - - -gatgcta
- - - - - - - - - - - -gatgtgg
- - - - - - - - - - - - - - - - -gaatgcc
- - - - - - - - - - - - - - - - - - - - - - gtgcctg