Sequence
atgc intronic sequence ATGC exonic sequencegtaacctttctgcaattcagtttagaatgtctgaaggtgtgtgtgttcaggtgttctcaggaagtgacagtttactttattctgtttcccagTTCACCTTGCTAGGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTTCATCACCCAAAGTGTGACGTCTGCCTTCAATTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g16090.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g16090.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G160198_T02 (Zea mays), 3'ss of exon 5
gtaacc---tttctgcaattcagtttagaatgtctgaaggtgtgtgtgttcaggtgttctcaggaagtgacagtt--tactttattc-tgtttcccagTTCACCTTGCTAGGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTTCATCACCCAAAGTGTGACGTCTGCCTTCAATTT
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gtaactaagctcttgcattttctttcatcgtggaagtgtgttacagtgtt-accagagatgagatcatatccgttattactttcgtcgtgccttccagTTCACCTTGCTGGGTACGGATTCGTACCACAAGCTGTGCTACAAGGAGCTGCATCATCCAAAGTGCGACGTCTGCCTTCAGTTT
upper sequence: LOC_Os03g16090.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G160198_T01 (Zea mays), 3'ss of exon 5
gtaacc---tttctgcaattcagtttagaatgtctgaaggtgtgtgtgttcaggtgttctcaggaagtgacagtt--tactttattc-tgtttcccagTTCACCTTGCTAGGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTTCATCACCCAAAGTGTGACGTCTGCCTTCAATTT----------------
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gtaactaagctcttgcattttctttcatcgtggaagtgtgttacagtgtt-accagagatgagatcatatccgttattactttcgtcgtgccttccagTTCACCTTGCTGGGTACGGATTCGTACCACAAGCTGTGCTACAAGGAGCTGCATCATCCAAAGTGCGACGTCTGCCTTCAGTTTGTAAGGCCTCGTGTCC
upper sequence: LOC_Os03g16090.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G151934_T02 (Zea mays), 3'ss of exon 5
gtaacctttctgcaattcagtttagaatgtctgaaggtgtgtgtgttcaggtgttctcaggaagtgacagtt--tactttattctgtttcccagTTCACCTTGCTAGGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTTCATCACCCAAAGTGTGACGTCTGCCTTCAATTT
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gcatgcaagctac--tccccctccctccatttcaagttaca-gtgttagtatcagagatggtaatacccgttcttgtttcttcctgttctccagTTCACATTGCTGAGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTGCACCATCCGAAATGCGACGTCTGCCTTCAGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtgtgttcaggtgttctcaggaagtgacagtttactttattctgtttcccagTTCACCTTGCTAGGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTTCATCACCCAAAGTGTGACGTCTGCCTTCAATTT
ctttattctgtttccc CT-rich tract
tttactttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacctttctgcaattcagtttagaatgtctgaaggtgtgtgtgttcaggtgttctcaggaagtgacagtttactttattctgtttcccagTTCACCTTGCTAGGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTTCATCACCCAAAGTGTGACGTCTGCCTTCAATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT