Sequence
atgc intronic sequence ATGC exonic sequence...catattttgcacatcagatttgttattcactatgattagtttagctgattaaagtttgaaccctgaattcttataaatatctgttatgacaatgtgtaagGTTCGTGAGTTGGCTGAAAAGGAGTCTGAAAACGGTGTCTTCAGACTACTCCGAAGTGATGTTACTCGGTTCCTTACCACAATACTTATTGGCACAAC
Basic information
species | Glycine max |
transcript | GLYMA02G46780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 1
---catattttgcacatcagatttgttattcactat-gattagt--ttagctgattaaagtttgaaccctgaattcttataaatatctgttatgacaatgtgtaagGTTCGTGAGTTGGCTGAAAAGGAGTCTGAAAACGGTGTCTTCAGACTACTCCGAAGTGATGTTACTCGGTTCCTTACCACAATACTTATTGGCACAAC
| | ||| |||| | ||| | || | | || | | | || | || | ||| | || |||| | | || | | | ||||||||||||||||||||||||| ||||||| ||||| |||||| | |||||||||||||||||||| ||||| || || ||||| |||||||||||
gtccccaccttgtttatca--tccattaaaccctgttggttgatggtagtccttttcatgtctaaacaattgatgcttaga----tttggttttctgttccactagGTTCGTGAGTTGGCTGAAAAGGAACCTGAAAATGGTGTTTTCAGAATGCTCCGAAGTGATGTTACTCGCTTCCTGACAACCATACTCATTGGCACAAC
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 1
catattttgcacatcagatttgttattcactatgattagtttagctgattaaagtttgaaccct---gaattcttataaatat-----ctgttatgacaatgtgtaagGTTCGTGAGTTGGCTGAAAAGGAGTCTGAAAACGGTGTCTTCAGACTACTCCGAAGTGATGTTACTCGGTTCCTTACCACAATACTTATTGGCACAAC
|| ||| || | ||| || || | | || | || ||| |||| || | || | | | | || ||| | | | |||| |||||||| ||||||||||||||||| || |||||||||| | | ||||| |||||||||||||| ||| | || || |||||||| ||||||||
-----cttatgtatctagattacttttct---tgtttcatctccctagtaaatgttctaacctattggagattttgtgattgtgttggttgatattgttttatatcagGTGCGTGAGTTAGCTGAAAAGGAGTCTGAGAATGGTGTCTTCAAAATGCTCCGCAGTGATGTTACTCGTTTCTTAACGACTATACTTATAGGCACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattaaagtttgaaccctgaattcttataaatatctgttatgacaatgtgtaagGTTCGTGAGTTGGCTGAAAAGGAGTCTGAAAACGGTGTCTTCAGACTACTCCGAAGTGATGTTACTCGGTTCCTTACCACAATACTTATTGGCACAAC
agctgat putative branch site (score: 4)
aattcttataaatatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catattttgcacatcagatttgttattcactatgattagtttagctgattaaagtttgaaccctgaattcttataaatatctgttatgacaatgtgtaagGTTCGTGAGTTGGCTGAAAAGGAGTCTGAAAACGGTGTCTTCAGACTACTCCGAAGTGATGTTACTCGGTTCCTTACCACAATACTTATTGGCACAAC
- - - - -cacatca
- - - - - - - - - - - - - - - - - - - - - -gctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttatg