Sequence
atgc intronic sequence ATGC exonic sequencegtggatgttattccatagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttgcatatttgattttatccatttacttatctgtattggtcgattgatttatatgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTAATAAATGCCAACAAGGTGGGGGAATCACCTGAGGAAATTGCTGCTTTCT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g14260.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 3
gtggatgttattcca-tagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttgcatatttgattttatccatttacttatctgtat-tggtcgattgatttata-tgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTAATAAATGCCAACAAGGTGGGGGAATCACCTGAGGAAATTGCTGCTTTCT
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gtggatgatactatactagttattt---tgctttcaattcttagcgggaatgtgcttg----------ttgctatacaacttgctgcatctccagttctcgattgtttttgttgattcgtttcttcttatatggttgattaattattgctgaataacagGAGGGTATCTATTTGTTTAATCGGAAGCCGAAGAAGGGGATTGAGTTCCTTGTTAATGCAAGCAAGGTGGGGGAGACACCAGAGGAGATAGCTGCGTTCC
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 3
gtggatgttattccatagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttg-catatttgattttatccatttacttatctgtattggtcgattgatttatatgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTAATAAATGCCAACAAGGTGGGGGAATCACCTGAGGAAATTGCTGCTTTCT
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----------------------------------------------------------------------gtaaacaaatgaacaaggttttgttaataaagtatatctttgctgtagcttttttaccaatga--agctaatgcaagtgtatggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAACAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 3
gtggatgttattccatagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttgcatatttgat-tttatccatttacttatctgtattggtcgattgatttatatgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTAATAAATGCCAACAAGGTGGGGGAATCACCTGAGGAAATTGCTGCTTTCT
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--------------------------------------------------------------gtaaccaagtgcagaaattttggaattgcaagtagatctctgttatttctgcaactgtttgac-atctaggaagctaatgctaagtttatggcagGAAGGTATATCACTTTTTAACAGGAAGCCGAAGAAAGGAATTGAATTCCTCATCAATGCCAACAAAGTGGGTAATTCACCAGAGGAAATAGCTGCTTTTC
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 4
gtggatgttattccatagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttg-catatttgattttatccatttacttatctgtattggtcgattgatttatatgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTAATAAATGCCAACAAGGTGGGGGAATCACCTGAGGAAATTGCTGCTTTCT
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----------------------------------------------------------------------gtaaacaaatgaacaaggttttgttaataaagtatatctttgctgtagcttttttaccaatga--agctaatgcaagtgtatggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTCMapped 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|88969992|gb|CI383494.1|CI383494EST: CAGAGGCTGCATCTTTGGAGCAGCGCCGAGCTTACAAGATGGAACTTCAG GAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTA
genomic: CAGAGGCTGCATCTTTGGAGCAGCGCCGAGCTTACAAGATGGAACTTCAGgtggatgtta ... tgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattttatccatttacttatctgtattggtcgattgatttatatgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTAATAAATGCCAACAAGGTGGGGGAATCACCTGAGGAAATTGCTGCTTTCT
gattgat putative branch site (score: 4)
attgatttatatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggatgttattccatagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttgcatatttgattttatccatttacttatctgtattggtcgattgatttatatgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTAATAAATGCCAACAAGGTGGGGGAATCACCTGAGGAAATTGCTGCTTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT