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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcatcatcctgctaatccatcaattaattaatgcatgatggtagaccaaagctacagtgttcttactgcatggatgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG

Basic information

species Zea mays
transcript GRMZM5G885392_T01
intron # 9
splice site 3'
intron type U2

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|18178811|gb|BM380021.1|BM380021
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|88748429|gb|DY532570.1|DY532570
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|71760700|gb|DR958637.1|DR958637
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|86468794|gb|DY235164.1|DY235164
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|78074964|gb|DV503398.1|DV503398
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTTTTGATTGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|148942558|gb|EC887577.2|EC887577
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAAATTTTTGATTGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|211475315|gb|FL222267.1|FL222267
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|110538710|gb|EE042664.1|EE042664
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTTTTGATTGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|211475316|gb|FL222268.1|FL222268
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 29 (downstream exon)
Score: 11

TTGTGGCACTGAGTTGGAGTACGACTCTTCAACCCGATTGATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 94

TTGTGGCACTGAGTTGGAGTACGACTCTTCAACCCGATTGATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG


Block sizes: 25 (upstream exon), 25 (downstream exon)
Score: 1

TTGTGGCACTGAGTTGGAGTACGACTCTTCAACCCGATTGATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 109

TTGTGGCACTGAGTTGGAGTACGACTCTTCAACCCGATTGATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgcatgatggtagaccaaagctacagtgttcttactgcatggatgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG
                               ttcttac  putative branch site (score: 109)
                                              tgttcct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcatcatcctgctaatccatcaattaattaatgcatgatggtagaccaaagctacagtgttcttactgcatggatgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG