Sequence
atgc intronic sequence ATGC exonic sequence...tatagtatgcccttttcagcccttaagttccatcgatttcataaaatactgttgaacatctcatgggagcatagttgattttgatggttctatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g31830.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g31830.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G075051_T01 (Zea mays), 3'ss of exon 4
tatagtatgcccttttcagcccttaagttccatcgatttcataaaatactgttga-acatctcatgggagc-atagttgattttgatggttctatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG
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-acattctgaagttctaaaaagtaaaactg-atgggttccttaggggagaataactacagttcctacttcctatatctgattttgatgtcctcatcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAATATGGATGTCTGTTTCTTGAGAGCAGTGCAAAAACACGAGAAAACGTTG
upper sequence: LOC_Os10g31830.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G809265_T02 (Zea mays), 3'ss of exon 4
tatagtatgcccttttcagcccttaagttccatcgatttcataaaatactgttga-acatctcatgggagc-atagttgattttgatggttctatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG
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-acattctggagttgtaaaaagtcaaactg-gtgggctctttaaggtagaataactacagttcatacttcctatttctgattttgatggtctcatcttgcagGATGATGAAAGAATGGTCACAGAAGAAGAAGGTCTTGCTTTTGCTGAAGAATCTGGTTGTCTGTTTCTTGAGAGCAGTGCAAAAACACGAGAAAATGTTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86839153|gb|CI331447.1|CI331447EST: TAGGACAATTACTAGTTCTTACTACAGAGGTGCTCAAGGCATTATTCTAG GAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAA
genomic: TAGGACAATTACTAGTTCTTACTACAGAGGTGCTCAAGGCATTATTCTAGgtaaataaca ... tatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atactgttgaacatctcatgggagcatagttgattttgatggttctatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG
ttttgat putative branch site (score: 4)
ttctatctttc putative PPT
ttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatagtatgcccttttcagcccttaagttccatcgatttcataaaatactgttgaacatctcatgggagcatagttgattttgatggttctatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG
- - -tatgccc
- - - - - - - - - - - - - - - - - - - -cataaaa
- - - - - - - - - - - - - - - - - - - - - - - - ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatgg