Sequence
atgc intronic sequence ATGC exonic sequence...gttttcatatcatgaatccttttcatagttttcaaaggaaaatgactatttaacaacttgaagctaaatatggttgctaatattattctgcccaattcagGTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAG
Basic information
species | Glycine max |
transcript | GLYMA12G07890.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 4
gttttcatatcatgaatcc-ttttcatagttttcaaaggaaaatgactatttaacaacttgaagctaaatatggttgctaatattattctgc--ccaattcagGTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAG
|| || | | || | | ||| ||| | | || || || | | | || || | || | |||| | | ||||||||||||| |||||| | ||||| ||||| || ||||||||||| |||
--ttgtattttaagagttagtggacatcaattttataataagatagg-atatgtcttttcacagtaaagttaccttcccttcattacttcattacttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
upper sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 7
--gttttcatatc-atgaatccttttcatagttttcaaaggaaaatgactatt-taacaacttgaagctaaatatggttgctaatattattctgcccaattcagGTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAG
|| | | | || | || | || || | | || |||| ||| | || || |||| | | | | | | | | | |||||| || ||||||||| | ||||| ||||||||||||||||||||||||
ctagttgcttgtagatagaggctactaat-gtgcagatatctttatttctatggtaatgagttaaactgaaattt--cttgtggttgtgtatcacttgagt-agGTAAGAAATTCTGGAACCTCTTTCACTTGCAGCCTATGCGTGATCAGAAG
upper sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 9
lower sequence: AT3G45780.1 (Arabidopsis thaliana), 3'ss of exon 8
gttttcatatcatgaatccttttcatagttttcaaaggaaaatgactatttaacaacttgaagctaaatatggttgctaatattattctgcccaattcagGTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAG
| | || ||| ||| || | | | || || | || | | ||| | | || | | ||||| | | |||| || |||||||||||| | || || ||||| ||||||||||||||||||
--------gtactcgattttttcgata-ttcttagattaatctgtcgatc--attgtataaagttttaaat------ttacattatattctctgtggcagGAAAGAAGTTCTGGAACATTTTCCACTTGCAACCTATGCGTGATCAGAAG
upper sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 8
gttttcatatcatgaatccttttcatagttttcaaaggaaaatgacta-tttaacaacttgaagctaaatatggttgctaatattattctgcccaattcagGTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAG
|| || || || | ||| || | ||| | || ||| | ||| | | ||| | ||| | || | | |||| || |||||||||||| |||| ||| |||||||||||||||||||||||
gtgtttctacttggagaaaacataataacattaacagggttttctttaattttaatactgtcacttccataactattttaagtctgttgaaatcg-tccagGGAAGAAGTTCTGGAACCTGTTCCATCTGCAGCCTATGCGTGATCAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatttaacaacttgaagctaaatatggttgctaatattattctgcccaattcagGTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAG
tgctaat putative branch site (score: 2)
ttctgccc putative PPT
ttgctaatattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttcatatcatgaatccttttcatagttttcaaaggaaaatgactatttaacaacttgaagctaaatatggttgctaatattattctgcccaattcagGTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAG
- - - - - catgaat
- - - - - - - - - - - - - - - - - aaggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttgc