Sequence
atgc intronic sequence ATGC exonic sequencegtatttcttttgatcatttatcaatcttcacgttttcgccacaacctaatattatgtgtttgcattgctgccctgtttaggaaactaattggttcaagtcttttcttatagGTGGTTTCCTCGCACAGAGCGATCAAGTGCTGTCGGGATTGCAATGGCTGGTTTTCAGCTTGGCAATACCATTGGTTTACTTCTTTCCCCTATCATCATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g63290.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g63290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G856598_T02 (Zea mays), 3'ss of exon 2
------------------gtatttcttttgatcatttatcaatcttcacgttttcgccacaa---cctaatattatgtgtttgc----attgctgccctg-tttaggaaactaattggttcaagtcttttcttatagGTGGTTTCCTCGCACAGAGCGATCAAGTGCTGTCGGGATTGCAATGGCTGGTTTTCAGCTTGGCAATACCATTGGTTTACTTCTTTCCCCTATCATCATG
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gtatctacctttgtaacatcattccttttgactactc--catctccaactttttccccacaaaaacatattgttgtttggctgtgggaatttctgctaagatttatgtaagtgtttgcattggcccctttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG
upper sequence: LOC_Os01g63290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g06040.t01 (Vitis vinifera), 3'ss of exon 2
-------------gtatttcttttgatcatttatcaatct-tcacgttttcgccaca-acctaatattatg-tgtttgcattgctgccctgtttaggaaact-----aattggttcaagtcttttcttatagGTGGTTTCCTCGCACAGAGCGATCAAGTGCTGTCGGGATTGCAATGGCTGGTTTTCAGCTTGGCAATACCATTGGTTTACTTCTTTCCCCTATCATCATG
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gtaccaattaccaaagttgtagaaaattgttgtttgatgtatgatagatccgcgatttacatcatatcatggtcacagtgttgttcttgtgttaaaagatgttgaagaaactttttgaactttttcttttagATGGTTTCCTCAAACAGAACGATCCAGGGCTGTTGGAATTGCAATGGCTGGATTTCAGCTTGGCAGTGCAATTGGGCTTACGCTTGCTCCAATCCTCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttgcattgctgccctgtttaggaaactaattggttcaagtcttttcttatagGTGGTTTCCTCGCACAGAGCGATCAAGTGCTGTCGGGATTGCAATGGCTGGTTTTCAGCTTGGCAATACCATTGGTTTACTTCTTTCCCCTATCATCATG
aactaat putative branch site (score: 2)
tcttttcttat putative PPT
ttttcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcttttgatcatttatcaatcttcacgttttcgccacaacctaatattatgtgtttgcattgctgccctgtttaggaaactaattggttcaagtcttttcttatagGTGGTTTCCTCGCACAGAGCGATCAAGTGCTGTCGGGATTGCAATGGCTGGTTTTCAGCTTGGCAATACCATTGGTTTACTTCTTTCCCCTATCATCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT