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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgttctttacccaaacctaaggtcgaggggagcattcagaacactacccatcctctgcataaatgtatgttttaccctcttcccctctgaaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAGGAAGGCGAGGAGGAAGATGGCAGTGCAAGCGAGGGCGAGCACGGGGAGA

Basic information

species Zea mays
transcript GRMZM2G038066_T02
intron # 5
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|60344601|gb|DN211574.1|DN211574
EST:     CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAG                         AAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
genomic: CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
EST: gi|60351395|gb|DN218368.1|DN218368
EST:     CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAG                         AAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
genomic: CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
EST: gi|78104974|gb|DV523392.1|DV523392
EST:     CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAG                         AAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
genomic: CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
EST: gi|78023453|gb|DV491840.1|DV491840
EST:     CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCCAACAACAAAAAG                         AAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
genomic: CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
EST: gi|211270508|gb|FL357031.1|FL357031
EST:     CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCCAACAACAAAAAG                         AAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
genomic: CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
EST: gi|71303863|gb|DR788046.1|DR788046
EST:     CAATATCAAACCGAAGTCTAACAACAAAAAG                         AAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
genomic: CAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
EST: gi|211465755|gb|FL467271.1|FL467271
EST:     CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCCAACAACAAAAAG                         AAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
genomic: CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
EST: gi|60348743|gb|DN215716.1|DN215716
EST:     CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAG                         AAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG
genomic: CAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAG

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), 49 (downstream exon)
Score: 108

GGCTTTTGAAATTGTTAGTGGGAAGAGTGAAACCAAGGCACCAGCACCACCAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAGGAAGGCGAGGAGGAAGATGGCAGTGCAAGCGAGGGCGAGCACGGGGAGA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 49

GGCTTTTGAAATTGTTAGTGGGAAGAGTGAAACCAAGGCACCAGCACCACCAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAGGAAGGCGAGGAGGAAGATGGCAGTGCAAGCGAGGGCGAGCACGGGGAGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 37

GGCTTTTGAAATTGTTAGTGGGAAGAGTGAAACCAAGGCACCAGCACCACCAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAGGAAGGCGAGGAGGAAGATGGCAGTGCAAGCGAGGGCGAGCACGGGGAGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 26

GGCTTTTGAAATTGTTAGTGGGAAGAGTGAAACCAAGGCACCAGCACCACCAAGCAGTAGTAACCACAGCAATATCAAACCGAAGTCTAACAACAAAAAGgtgacatctg ... aaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAGGAAGGCGAGGAGGAAGATGGCAGTGCAAGCGAGGGCGAGCACGGGGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacccatcctctgcataaatgtatgttttaccctcttcccctctgaaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAGGAAGGCGAGGAGGAAGATGGCAGTGCAAGCGAGGGCGAGCACGGGGAGA
                         ttttaccctcttcccc  CT-rich tract
              ataaatgtatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgttctttacccaaacctaaggtcgaggggagcattcagaacactacccatcctctgcataaatgtatgttttaccctcttcccctctgaaacgtgcagAAACCACCGGAGCCTAAGGTGAAGCAGCCAAAGCCGCGTGCCCCTGCAGAGGAAGGCGAGGAGGAAGATGGCAGTGCAAGCGAGGGCGAGCACGGGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - -acccaaa
- - - - - - - - - - - - - - - - gcattca
- - - - - - - - - - - - - - - - - - - - - cactacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcata