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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcgaattatgcccccattttcgtgttttgcccaaaatactcttattagggcatatattcatttggtgatttttcacatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGCAGCGTTGTCACTACACTCCGTACCGCCGCGCGCCGCCTGTCACTTTGCG

Basic information

species Zea mays
transcript GRMZM5G803610_T02
intron # 1
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|211168538|gb|FK982826.1|FK982826
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCA-GGC-GCGGAGGC
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
EST: gi|33467350|gb|CF244399.1|CF244399
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
EST: gi|78107382|gb|DV525800.1|DV525800
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
EST: gi|211168536|gb|FK982824.1|FK982824
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
EST: gi|211168540|gb|FK982828.1|FK982828
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
EST: gi|211170210|gb|FK982830.1|FK982830
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
EST: gi|211168537|gb|FK982825.1|FK982825
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
EST: gi|211168535|gb|FK982823.1|FK982823
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGARGC
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
EST: gi|74232550|gb|DT640464.1|DT640464
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGC
EST: gi|211168541|gb|FK982829.1|FK982829
EST:     TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTG                         GTAAATGATGGCAGTCATCCTGCCTA
genomic: TGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTA

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: 44 (upstream exon), 46 (downstream exon)
Score: 7

CACTGCTGATCCCTCGACTGTGTCTTTTCGCTTTGGAGCTCGAGGAAGCTTGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGCAGCGTTGTCACTACACTCCGTACCGCCGCGCGCCGCCTGTCACTTTGCG


Block sizes: 20 (upstream exon), 30 (downstream exon)
Score: 1

CACTGCTGATCCCTCGACTGTGTCTTTTCGCTTTGGAGCTCGAGGAAGCTTGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGCAGCGTTGTCACTACACTCCGTACCGCCGCGCGCCGCCTGTCACTTTGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 6

CACTGCTGATCCCTCGACTGTGTCTTTTCGCTTTGGAGCTCGAGGAAGCTTGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGCAGCGTTGTCACTACACTCCGTACCGCCGCGCGCCGCCTGTCACTTTGCG


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 6

CACTGCTGATCCCTCGACTGTGTCTTTTCGCTTTGGAGCTCGAGGAAGCTTGCCTTGCCATCCGCCACAGCAGGCTCATCCATCAGGATCTACTAATTTGgtttcgaatt ... acatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGCAGCGTTGTCACTACACTCCGTACCGCCGCGCGCCGCCTGTCACTTTGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccaaaatactcttattagggcatatattcatttggtgatttttcacatactcagGTAAATGATGGCAGTCATCCTGCCTAGGACCGTCCGCAGGGCGGCGGAGGCAGCGTTGTCACTACACTCCGTACCGCCGCGCGCCGCCTGTCACTTTGCG
                                       tttttcac  CT-rich tract
                      atatattcattt  TA-rich tract