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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcgtgagacccaaaaaaaaaagggaaaaaaggacacagatcttttcttgattaaaaaaatgttattatttgctaagcagtcattggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTCCCAAG

Basic information

species Zea mays
transcript GRMZM5G816432_T01
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|211541384|gb|FL468171.1|FL468171
EST:     CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATT                         ATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
genomic: CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
EST: gi|31406396|gb|CD485128.1|CD485128
EST:     CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATT                         ATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
genomic: CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
EST: gi|5713652|gb|AI943644.1|AI943644
EST:     CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATT                         ATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
genomic: CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
EST: gi|211468297|gb|FL467296.1|FL467296
EST:     CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATT                         ATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
genomic: CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
EST: gi|211394252|gb|FL456747.1|FL456747
EST:     CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATT                         ATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
genomic: CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
EST: gi|78025784|gb|DV494171.1|DV494171
EST:     CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATT                         ATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC
genomic: CAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTC

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: 48 (upstream exon), 47 (downstream exon)
Score: 54

GTGGAACAGTCACTGCAGCAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTCCCAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 54

GTGGAACAGTCACTGCAGCAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTCCCAAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 49

GTGGAACAGTCACTGCAGCAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTCCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

GTGGAACAGTCACTGCAGCAGTTGATCTGGTTATGGAACGTGGAGCTGAAATCAGTCAGATAAAAATTgtgagttcgt ... tggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTCCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttttcttgattaaaaaaatgttattatttgctaagcagtcattggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTCCCAAG
      tcttgat  putative branch site (score: 254)
        ttgattaaaaaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcgtgagacccaaaaaaaaaagggaaaaaaggacacagatcttttcttgattaaaaaaatgttattatttgctaagcagtcattggtatgcagATATCAGCTGTTGCTGCCCCTCCTGCCCTCAAGAAGCTCAATCAAAGATTCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA