Sequence
atgc intronic sequence ATGC exonic sequencegtgctcaattatcaattttttttcatgctcactatacctttatttaaatgcaaaatggtctaatctttttctttttgaaaggaacatagtctaaatcattttggttgttccctatgtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g47410.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g47410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 7
----------gtgctcaattatcaattttttttcatgctcactat----acctttatttaaatgcaaaatggtctaatctt-----tttctttttgaaagga-----acatagtctaaatcatttt-------ggttgttccctatgtgtca--ttagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACG
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gtgagacccctcttgaaaccattgtgtgctttataaaccaaaaagtaggaaattggaggaaagaaggaaaagcctagatttagagacctttttttaatggtataagcacataattagtatgattattatgtcagtttgacacaagcataccacctcagGGTACTGTGCCGGAGGTTGTGCAGCAATTGCAGATTCTGGAACTTCTTTGTTGGCAGGTCCAACG
upper sequence: LOC_Os01g47410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ34433 (Selaginella moellendorffii), 3'ss of exon 5
gtgctcaattatcaattttttttcatgctcactatacctttatttaaatgcaaaatggtctaatctttttctttttgaaaggaacatagtctaaatcattttggttgttccctatgtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACG
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--------------------------------------------------------------gttatatcataatggcttgctatacgcactaggtcttaatggtttt-------atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGTTGGTCCTACG
upper sequence: LOC_Os01g47410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ06917 (Selaginella moellendorffii), 3'ss of exon 5
gtgctcaattatcaattttttttcatgctcactatacctttatttaaatgcaaaatggtctaatctttttctttttgaaaggaacatagtctaaatcattttggttgttccctatgtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACG
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--------------gcagttcaacatgggagatgtggctgtggatggccagagcacaggtta----tatcataatggcttgctatatgcactagttc---ttaatggtttcatgtttgc----agGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG
upper sequence: LOC_Os01g47410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ34434 (Selaginella moellendorffii), 3'ss of exon 5
gtgctcaattatcaattttttttcatgctcactatacctttatttaaatgcaaaatggtctaatctttttctttttgaaaggaacatagtctaaatcattttggttgttccctatgtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACG
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-------------------------------------------------------------------gttatatcataatggcttgctatatgcactaattc--ttaatggatttatgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG
upper sequence: LOC_Os01g47410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ34432 (Selaginella moellendorffii), 3'ss of exon 5
gtgctcaattatcaattttttttcatgctcactatacctttatttaaatgcaaaatggtctaatctttttctttttgaaaggaacatagtctaaatcattttggttgttccctatgtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACG
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-------------------------------------------------------------------gttatatcataatggcttgctatatgcactagttc--ttaatggttttatgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGTTGGTCCTACGMapped 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|2799538|gb|AA752527.1|AA752527EST: TTCAATATGGGCGATGTCCTAATTGGAGGGAATTCCACAG GATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGC
genomic: TTCAATATGGGCGATGTCCTAATTGGAGGGAATTCCACAGgtgctcaatt ... gtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGC
EST:
gi|2799301|gb|AA752290.1|AA752290EST: TTCAATATGGGCGATGTCCTAATTGGAGGGAATTCCACAG GTTTCTGTGCAGCTGGGTGTGCAGCAAATAGCAGATTCTTGGAACTTCACT
genomic: TTCAATATGGGCGATGTCCTAATTGGAGGGAATTCCACAGgtgctcaatt ... gtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAA-TAGCAGATTCT-GGAACTTCACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttgaaaggaacatagtctaaatcattttggttgttccctatgtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACG
gtctaaa putative branch site (score: 3)
taaatcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctcaattatcaattttttttcatgctcactatacctttatttaaatgcaaaatggtctaatctttttctttttgaaaggaacatagtctaaatcattttggttgttccctatgtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT