Sequence
atgc intronic sequence ATGC exonic sequence...tcagctatatttggcaagcatgtggtagatcattttatctatcaagttgttttgtggtatatttgtaaacataatgacaactctgccctggttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g34300.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g34300.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G484880_T01 (Zea mays), 3'ss of exon 6
-------tcagctatatttggcaagcatgtggtagatcattttatctatcaagttgttttgtg-gtatatttgtaaacataatgacaactctgccctggttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGG
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ctgactcaaaattcaatgttttagctatctgctttagcaaattaagagactaacaaaccactgtgcttatcttgtaacatattaattactat-ctctgaa-gATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGC------
upper sequence: LOC_Os11g34300.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G484880_T02 (Zea mays), 3'ss of exon 6
-tcagctatatttggcaagcatgtggtagatcattttatctatcaagttgttttgtg-gtatatttgtaaacataatgacaactctgccctggttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGG
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caaaattcaatgttttagctatctgctttagcaaattaagagactaacaaaccactgtgcttatcttgtaacatattaattactat-ctctgaa-gattcagGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGG
upper sequence: LOC_Os11g34300.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G484880_T03 (Zea mays), 3'ss of exon 6
tcagctatatttggcaagcatgtggtagatcattttatctatcaagttgttttgtggtatatttgtaaacataatgacaactctgccctggttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGG-----
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-------------------------------------actaacaaaccactgtgct---tatcttgtaacatattaattactat-ctctgaa-gattcaggacaaggaaaaaagatcatcacatagtctactagtgttgcagTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG
upper sequence: LOC_Os11g34300.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G484880_T05 (Zea mays), 3'ss of exon 6
tcagctatatttggcaagcatgtggtagatcattttatctatcaagttgttttgtggtatatttgtaaacataatgacaactctgccctggttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGG
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-------------------------------------actaacaaaccactgtgct---tatcttgtaacatattaattactat-ctctgaa-gattcaggacaaggaaaaaagatcatcacatagtctactagtgttgcagTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGG
upper sequence: LOC_Os11g34300.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0129g01020.t01 (Vitis vinifera), 3'ss of exon 6
tcagctatatttggcaagcatgtggtagatcattttatctatc---aagttgtt--ttgtggtatatttgtaaacataa-tgacaactctgccctggttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGG---
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-------cattcataaactgttcaatattttgctttgctttttttagggctgttaaccagggttgattttgatagttaagcgctaagtgtggttttat--atttgttagAAGGACAATGCATCAACAGAAAAGCTTGTCAAGATCCCAATTCCAGCGACACTAAAGAAGCAACTTGTTGATGATTGGGATTTTGTTACTCAGCAGGATAMapped 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|88415243|gb|CI584066.1|CI584066EST: AAACTGCAGTCAAGGGGAAGAAACGCAAAAGTCAGCCTGGTGGGACTGAG GAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTATCCTTCA
genomic: AAACTGCAGTCAAGGGGAAGAAACGCAAAAGTCAGCCTGGTGGGACTGAGgtgtctctca ... gttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCA
EST:
gi|88415227|gb|CI584050.1|CI584050EST: AAACTGCAGTCAAGGGGAAGAAACGCAAAAGTCAGCCTGGTGGGACTGAG GAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTATCCTTCA
genomic: AAACTGCAGTCAAGGGGAAGAAACGCAAAAGTCAGCCTGGTGGGACTGAGgtgtctctca ... gttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgttttgtggtatatttgtaaacataatgacaactctgccctggttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGG
ggttgat putative branch site (score: 5)
tatatttgtaaacata 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
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tcagctatatttggcaagcatgtggtagatcattttatctatcaagttgttttgtggtatatttgtaaacataatgacaactctgccctggttgatccagGAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG