Sequence
atgc intronic sequence ATGC exonic sequence...tcgcttagtactatgtacagaagggaggagccgtatgaggtgaaaacctcatgtacggttttggaacggagattttttgaatagaacgaacgaccgtaacGGATGTTGGCTCAATCCGAAGGAAATTATGCGGAAGCTTTGCAAAATTATTATGAAGCTACGCGACTAGAAAGTGATCCCTATGATCGAAGTTATATACT
Basic information
species | Oryza sativa |
transcript | LOC_Osp1g00350.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Osp1g00350.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0000g01770.t01 (Vitis vinifera), 3'ss of exon 1
----tcgcttagtactatgtacagaagggaggagccgtatgaggtgaaaacctcatgtacggttttggaacggagattttttgaatagaacgaacgaccgtaacGGATGTTGGCTCAATCCGAAGGAAATTATGCGGAAGCTTTGCAAAATTATTATGAAGCTACGCGACTAGAAAGTGATCCCTATGATCGAAGTTATATACT
| || | |||| || || | ||||| ||||||| |||||| |||| || |||||||||| ||||||||| || || ||| ||| || || ||| || | ||||||||||||| |||||||| | || |||||||||| ||||| | |||||| ||||||| || || |||||| ||
tgtattatttt-cattatgcacgtaatgaaggagttgtatgagatgaaaatctcaaatatagttttggaacaaagatttttttaaatga-----cgatgataatagACGTCAACTCGATTCCAAGGAAATTATGCAGAAGCTTTATATAACTATTATGAAGTTACGCAATTAGAAATTGATCCCCATAATGAAAGTTACAT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctcatgtacggttttggaacggagattttttgaatagaacgaacgaccgtaacGGATGTTGGCTCAATCCGAAGGAAATTATGCGGAAGCTTTGCAAAATTATTATGAAGCTACGCGACTAGAAAGTGATCCCTATGATCGAAGTTATATACT
attttttgaatagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgcttagtactatgtacagaagggaggagccgtatgaggtgaaaacctcatgtacggttttggaacggagattttttgaatagaacgaacgaccgtaacGGATGTTGGCTCAATCCGAAGGAAATTATGCGGAAGCTTTGCAAAATTATTATGAAGCTACGCGACTAGAAAGTGATCCCTATGATCGAAGTTATATACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC