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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccggttatgaccctaacaacattgatttgtttaggatgcttagacttctttggttttctgattactgatgtaatccttatgtaaatcttactatttctttcagcagGAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGTGGAACCGACAGTATAGGACTAAGCTCTTTGCTCACTGACAGCCTGGATG

Basic information

species Zea mays
transcript GRMZM2G062230_T02
intron # 7
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|148928279|gb|EE284874.2|EE284874
EST:     AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATG                         C
genomic: AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGgtaccggtta ... ctttcagcag-
EST: gi|148928279|gb|EE284874.2|EE284874
EST:     AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATG                         C
genomic: AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGgtaccggtta ... ctttcagcag-
EST: gi|148928279|gb|EE284874.2|EE284874
EST:     AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATG                         C
genomic: AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGgtaccggtta ... ctttcagcag-
EST: gi|71757777|gb|DR955714.1|DR955714
EST:     AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATG                         GAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGT
genomic: AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGgtaccggtta ... ctttcagcagGAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGT
EST: gi|211104855|gb|FL162455.1|FL162455
EST:     AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGCAG                       
genomic: AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAAT---Ggtaccggtta ... ctttcagc
EST: gi|7242231|gb|AW574432.1|AW574432
EST:     AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATG                         GAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGT
genomic: AAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGgtaccggtta ... ctttcagcagGAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGT

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: 47 (upstream exon), 31 (downstream exon)
Score: 5

CAATGTGCTACGGATGGTAGGAAAGAGGAACTAAACAGTCAAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGgtaccggtta ... ctttcagcagGAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGTGGAACCGACAGTATAGGACTAAGCTCTTTGCTCACTGACAGCCTGGATG


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

CAATGTGCTACGGATGGTAGGAAAGAGGAACTAAACAGTCAAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGgtaccggtta ... ctttcagcagGAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGTGGAACCGACAGTATAGGACTAAGCTCTTTGCTCACTGACAGCCTGGATG


Block sizes: 34 (upstream exon), 42 (downstream exon)
Score: 5

CAATGTGCTACGGATGGTAGGAAAGAGGAACTAAACAGTCAAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGgtaccggtta ... ctttcagcagGAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGTGGAACCGACAGTATAGGACTAAGCTCTTTGCTCACTGACAGCCTGGATG


Block sizes: 27 (upstream exon), 34 (downstream exon)
Score: 9

CAATGTGCTACGGATGGTAGGAAAGAGGAACTAAACAGTCAAACATCAGTAGAGGGCGATGGTATTAATGCAAAGCCAGAGATTTCAATGgtaccggtta ... ctttcagcagGAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGTGGAACCGACAGTATAGGACTAAGCTCTTTGCTCACTGACAGCCTGGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttctgattactgatgtaatccttatgtaaatcttactatttctttcagcagGAGTCAGCTGGTGACCCAGAGCGTGAAGCATCTTGCCCCAGACTCTTGGGTGGAACCGACAGTATAGGACTAAGCTCTTTGCTCACTGACAGCCTGGATG
                                  tcttactatttctttc  CT-rich tract
 taaatcttactattt  TA-rich tract