Sequence
atgc intronic sequence ATGC exonic sequenceGTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactgttcctctaaggttctgactatccacatttactgttgaaaattgtcatgtaggattgaatagaatcactacttatttataatttaccagagacgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttccttttgtattgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g29830.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G818643_T01 (Zea mays), 5'ss of exon 4
GTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactgttcctctaaggttctgactatccacatttactgttgaaaattgtcatgtaggattgaatagaatcactacttatttataatttaccagagacgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttccttttgtattgcag
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GTCACTGGGAAGGCGGTGATGCTTGACGAGATCATCAACTATGTCCAGTCCCTGCAAAGACAAGTCGAGgtaatcagtaacttgtatgttaaa-atacgcacaactttgtctcaatcaaggcttagctacgaaccaagtcttcatttggaagagaggaagtagaatcgct-------------------------------------------------------------------------
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G818643_T02 (Zea mays), 5'ss of exon 3
-------------------------------GTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactgttcctctaaggttctgactatccacatttactgttgaaaattgtcatgtaggattgaatagaatcactacttatttataatttaccagagacgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttccttttgtattgcag
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CAAATGAACATCTCTGTCCATTGGAATCCAGGTCACTGGGAAGGCGGTGATGCTTGACGAGATCATCAACTATGTCCAGTCCCTGCAAAGACAAGTCGAGgtaatcagtaacttgtatgttaaa-atacgcacaactttgtctcaatcaaggcttagctacgaaccaagtcttcatttggaagagaggaagtagaatcgct-------------------------------------------------------------------------
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G137541_T01 (Zea mays), 5'ss of exon 4
GTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactg-------ttcctctaaggttctgactatccacatttactgttgaaaattgtcatgtagga--ttgaatag--aatcactacttatttataatttaccagaga-cgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttc--cttttgtattgcag
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GTCACTGGCAAGGCGGTGATGCTTGACGAGATCATCAACTACGTTCAGTCCCTGCAAAGACAAGTTGAGgtaataacaaacatcccccccaatatatactgagacctgaatcaagttgtcatttgcaatagaggaagtagaacagctagacactgagaccctgaatatgaacacagttcctctttctacaaaaccctcgttacatacata-cataccgatggcaggcacatcaaaacactgaacgaatctcttgcag
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S68_190V6.1 (Physcomitrella patens), 5'ss of exon 3
-------------------------------GTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactgttcctctaaggttctgactatccacatttactgttgaaaat-tgtcatgtaggattgaataga-atcactacttat---ttataatttaccagagacgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttccttttgtattgcag
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CCTGCAGGACCTCGTACCCGGCTGCCGCAAAGTCACCGGCAAGGCAGTCATGCTTGACGAGATCATCAACTATGTTCAATCCCTCCAACGACAAGTTGAAgtatgtctcttacccattttcaacgcactgctaatgctattccattcatgtcttaggcacccttcttgttatcgctagtgatgaattgtagtctagtattgagttgtatcgtacactttgttatcttttttacag--------------------------------------------
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S226_51V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------------GTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactgtt--cctctaaggttctgactatc-cacatttactgttgaaaattgtcatgtaggattgaa-tagaatcactacttatttataatttaccagagacgtgtttctagtaactaattatgtctgccatggtaaaccacaaa-acggaaaatgctgaccttccttttgtattgcag
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CTTGCAGGACCTCGTTCCTGGGTGCAAGAAAGTTACGGGCAAAGCGGTCATGCTCGACGAGATCATCAACTATGTTCAATTCCTCCAGCGCCAAGTCGAAgtacgtctagcctctctctctctctctctcgttccttccttccttccaattcaggtctagcgtgggagtatatctaggagtaaatcagaacttcgggatgttccatgtcaagctttgatatgcccccaatttgtttcgcagcatctatcaatgaggctggcat-ccgtgtgctcag---
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S226_51V6.2 (Physcomitrella patens), 5'ss of exon 2
-------------------------------GTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactgtt--cctctaaggttctgactatc-cacatttactgttgaaaattgtcatgtaggattgaa-tagaatcactacttatttataatttaccagagacgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttccttttgtattgcag
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CTTGCAGGACCTCGTTCCTGGGTGCAAGAAAGTTACGGGCAAAGCGGTCATGCTCGACGAGATCATCAACTATGTTCAATTCCTCCAGCGCCAAGTCGAAgtacgtctagcctctctctctctctctctcgttccttccttccttccaattcaggtctagcgtgggagtatatctaggagtaaatcagaacttcgggatgttccatgtcaagc--tttgatatgcccccaatt-tgtttcgcag----------------------------------Mapped 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|218493872|gb|FG957202.1|FG957202EST: TGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAG TTCTTATCGATGAAGCTTGCGACAGTAAACCCAATGCTTGACCTCAACATA
genomic: TGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactgttcc ... tgtattgcagTTCTTATCGATGAAGCTTGCGACAGTAAACCCAAGGCTTGACCTCAACATA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactgttcctctaaggttctgactatccacatttactgttgaaaattgtcatgtaggattgaatagaatcactacttatttataatttaccagagacgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttccttttgtattgcag
- - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG