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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgctcactgcctgattgcggctctgacatttttccctcttattttcttctgagtttattatggtatatatctttctgctattggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAGGAATTGAAAG

Basic information

species Zea mays
transcript GRMZM2G089259_T01
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|74237070|gb|DT644984.1|DT644984
EST:     TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
genomic: TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
EST: gi|87157614|gb|DY402403.1|DY402403
EST:     TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
genomic: TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
EST: gi|71428557|gb|DR809607.1|DR809607
EST:     TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
genomic: TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
EST: gi|94475718|gb|EB704676.1|EB704676
EST:     TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
genomic: TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
EST: gi|87157722|gb|DY402511.1|DY402511
EST:     TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAA
genomic: TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
EST: gi|22819833|gb|BU499923.1|BU499923
EST:     TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAA
genomic: TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAA
EST: gi|76012907|gb|DT940077.1|DT940077
EST:     TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
genomic: TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
EST: gi|60356662|gb|DN223635.1|DN223635
EST:     TGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
genomic: TGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
EST: gi|26558674|gb|CA830909.1|CA830909
EST:     TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAAGTGGGAAACCTTAGC
genomic: TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGC
EST: gi|148994788|gb|EE034233.2|EE034233
EST:     TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAG                         ATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG
genomic: TCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAG

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: 140

TTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAGGAATTGAAAG


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

TTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAGGAATTGAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 24

TTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAGGAATTGAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 98

TTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGGTTCTGTCCATGATCAAGgttcgtgctc ... attggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAGGAATTGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcttattttcttctgagtttattatggtatatatctttctgctattggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAGGAATTGAAAG
                   tttattatggtatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtgctcactgcctgattgcggctctgacatttttccctcttattttcttctgagtttattatggtatatatctttctgctattggtgcagATCTATAGCTGGAGGAAGTGGGAAACCTTAGCAGGTCCAATTGCTGCTGAGGAATTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT