Sequence
atgc intronic sequence ATGC exonic sequence...aacttgcagagctgattccaggcatctatattttatactttctgctcagtgtgctgtatatctctgccatactgacctttgttctgtttattcatgttagATGTCGAAGTCTGCTCCTTCAGATCAGTCTCGTATTAACCTTCTTGATCCAAAAGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g54020.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 10
----------------------------------aacttgcagagctg-attccaggc--atctatattttat---actttctgctcagtgtgctgtatatctctgccatactgacctttgttctgtttattcatgttagATGTCGAAGTCTGCTCCTTCAGATCAGTCTCGTATTAACCTTCTTGATCCAAAAGAT
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gtgattgacagaactgccagtttagatatgcatttaattattgagttatgttctgagccgattcatattttttctggttacctgattactgtcctctatacatgtaatgtgatgacttctgttttg-------gtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT
upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 3'ss of exon 10
aacttgcagagctgattccaggcatctatattt-tatactttctgctcagtgtgctgtatatctctgccatactgacctttgttctgtttattcatgt-tagATGTCGAAGTCTGCTCCTTCAGATCAGTCTCGTATTAACCTTCTTGATCCAAAAGAT
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--cttctgatgtctattagacctctctttatttctacttttgtaaatgggtttcttttgttaccgaatgacaattcctttttcatttttcgtttgtctgtagATGTCCAAGTCTGCTTCTTCAGATCAGTCTCGTATCAACCTTCTTGACCCAAAAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagtgtgctgtatatctctgccatactgacctttgttctgtttattcatgttagATGTCGAAGTCTGCTCCTTCAGATCAGTCTCGTATTAACCTTCTTGATCCAAAAGAT
tactgac putative branch site (score: 1)
tttattc putative PPT
tttattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacttgcagagctgattccaggcatctatattttatactttctgctcagtgtgctgtatatctctgccatactgacctttgttctgtttattcatgttagATGTCGAAGTCTGCTCCTTCAGATCAGTCTCGTATTAACCTTCTTGATCCAAAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA