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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaatcctttaggccttctatacaactgcaggaatttcagcctggatgctgacaaagctggatggtgaatttcttgcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG

Basic information

species Zea mays
transcript GRMZM2G021378_T01
intron # 10
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|78075707|gb|DV504141.1|DV504141
EST:     CGGCGAGCAAATCTTTCAGAGAGCGATTNCA-GAGCAAGGGCGAGGAAGG                         GTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
genomic: CGGCGAGCAAATCTTTCAGAGAGCGATT-CAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
EST: gi|89250950|gb|DY622736.1|DY622736
EST:     TCAAGAGCAAGGGCGAGGAAGG                         GTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
genomic: TCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
EST: gi|78109316|gb|DV527732.1|DV527732
EST:     ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGG                         GTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
genomic: ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
EST: gi|76289341|gb|DV028909.1|DV028909
EST:     ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGG                         GTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
genomic: ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
EST: gi|76928325|gb|DV171578.1|DV171578
EST:     ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGG                         GTACTGGACACGCTGCA
genomic: ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCA
EST: gi|76289342|gb|DV028910.1|DV028910
EST:     CGGCGAGCAAATCTTTCAGAGAGCGATTTCA-GAGCAAGGGCGAGGATGG                         GTACTGGACACGCTGCAG
genomic: CGGCGAGCAAATCTTTCAGAGAGCGATT-CAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAG
EST: gi|78124413|gb|DV542797.1|DV542797
EST:     ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGG                         GTACTGGACCCGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
genomic: ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
EST: gi|78075706|gb|DV504140.1|DV504140
EST:     ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGG                         GTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG
genomic: ACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAG

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: 24 (upstream exon), 44 (downstream exon)
Score: 6

ACAATCGACAAGCTGATAGAAACAGGCGACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 416

ACAATCGACAAGCTGATAGAAACAGGCGACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 733

ACAATCGACAAGCTGATAGAAACAGGCGACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 59

ACAATCGACAAGCTGATAGAAACAGGCGACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcc ... gcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatttcagcctggatgctgacaaagctggatggtgaatttcttgcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG
                tgctgac  putative branch site (score: 59)
                                       tttcttgc  putative PPT
                                     aatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaatcctttaggccttctatacaactgcaggaatttcagcctggatgctgacaaagctggatggtgaatttcttgcattcacagGTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG