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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacgaacataggcgctcaagtttggacttgctatgagttcgttgctctgtcactatgcgtggtgatgaactctgtaacgttggaagtaattggtttgcccttcttctttttgtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA

Basic information

species Zea mays
transcript GRMZM2G165535_T05
intron # 4
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|32919710|gb|CF024522.1|CF024522
EST:     GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAG                         TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
genomic: GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
EST: gi|71771666|gb|DR969603.1|DR969603
EST:     GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAG                         TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
genomic: GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
EST: gi|148950412|gb|EC895979.2|EC895979
EST:     GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAG                         TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
genomic: GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
EST: gi|14646044|gb|BI180233.1|BI180233
EST:     GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAG                         TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
genomic: GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
EST: gi|148943663|gb|EC888727.2|EC888727
EST:     GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAG                         TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
genomic: GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
EST: gi|76280415|gb|DV019983.1|DV019983
EST:     GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAG                         TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
genomic: GGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA
EST: gi|32801826|gb|CD954062.1|CD954062
EST:     GATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAG                         TTATTACTGAATATGACTACGTCTTCTCCGAAAACGGCCTGGATGCACACA
genomic: GATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACA

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: 49 (upstream exon), 49 (downstream exon)
Score: 142

CATGTGACAGTGGGCGTGGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

CATGTGACAGTGGGCGTGGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 266

CATGTGACAGTGGGCGTGGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 306

CATGTGACAGTGGGCGTGGTTGGCGGATCCGATCTGGTGAAGATTACCGAGCAGCTCGGCAGTACAGgtgacgaaca ... gtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactctgtaacgttggaagtaattggtttgcccttcttctttttgtttttgcagTTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA
     ctgtaac  putative branch site (score: 306)
                       ttggtttgcccttctt  putative PPT
                                     ttctttttgttttt  TA-rich tract