Sequence
atgc intronic sequence ATGC exonic sequence...caacagaaatgggggtacctaattcaaaccaaacctgtgcaattttatcatcacaataactgaattttgatatgtttttcttcttcattgttgttttcagGCGGCAGCAGCAGCTAGCTCCTTACAAGCTAAAGTGTGATAAAGAACCACTTAATAACAA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g45400.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G114459_T01 (Zea mays), 3'ss of exon 2
-caacagaaatgggggtacctaattcaaaccaaacctgtgcaattttatcatcacaataactgaattttgatatgtttttcttcttcat--tgttgt-tttcagGCGGCAGCAGCAGCTAGCTCCTTACAAGCTAAAGTGTGATAAAGAACCACTTAATAACAA
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ctctttcagttctctatttcttttttatattttgcctgtgcatttt--cccccatggtgat--gattctgatacctttttctccctaatacccctgtatttcagGCGGCAGCAGCAGCTAACTCCGTACAAGCTAAAGTGTGACAAGGACCCACTTAATAACAA
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G828278_T01 (Zea mays), 3'ss of exon 1
-caacagaaatgggggtacctaattcaaaccaaacctgtgcaattttatcatcacaataactgaattttgatatgtttttcttctt--cattgttgt-tttcagGCGGCAGCAGCAGCTAGCTCCTTACAAGCTAAAGTGTGATAAAGAACCACTTAATAACAA----------------------------------------
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cttccagtactcta--tttcttgtttatattttgcttgtgcatttttcttcccacagtggt--gattctgatatctttttctccctaacacccctgtctttcagGCGGCAGCAGCAGCTAGTTCCATACAAGCTAAAGTGTGACAAAGATCCACTTAATAACAAGTATGTCTAACTTATCGACCAAAGCCACTTCACATCAATG
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G828278_T02 (Zea mays), 3'ss of exon 1
-caacagaaatgggggtacctaattcaaaccaaacctgtgcaattttatcatcacaataactgaattttgatatgtttttcttctt--cattgttgt-tttcagGCGGCAGCAGCAGCTAGCTCCTTACAAGCTAAAGTGTGATAAAGAACCACTTAATAACAA
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cttccagtactcta--tttcttgtttatattttgcttgtgcatttttcttcccacagtggt--gattctgatatctttttctccctaacacccctgtctttcagGCGGCAGCAGCAGCTAGTTCCATACAAGCTAAAGTGTGACAAAGATCCACTTAATAACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatcacaataactgaattttgatatgtttttcttcttcattgttgttttcagGCGGCAGCAGCAGCTAGCTCCTTACAAGCTAAAGTGTGATAAAGAACCACTTAATAACAA
tttttcttcttcattg CT-rich tract
aattttgatatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caacagaaatgggggtacctaattcaaaccaaacctgtgcaattttatcatcacaataactgaattttgatatgtttttcttcttcattgttgttttcagGCGGCAGCAGCAGCTAGCTCCTTACAAGCTAAAGTGTGATAAAGAACCACTTAATAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
caacaga
- - - - - - - - - - - - -aaaccaa
- - - - - - - - - - - - - - - - -cctgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - -cacaata