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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcaaattcatcatagctgtcctttgccctgcaggaatctgagcctacagtatagcctaaccttgtttgtgtagttcgtgtagttcacagtgggagacgcatgtgccatcttgatgagttaaatgccgaacttgtttctttgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTGTCGACGCACAAAACATCTCCGCTGGGTGGAGATTTCAATGGCACAACTC

Basic information

species Zea mays
transcript GRMZM2G411333_T01
intron # 9
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|5871584|gb|AW018055.1|AW018055
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGCCAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|71309093|gb|DR790816.1|DR790816
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|78105425|gb|DV523843.1|DV523843
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|6031461|gb|AW076363.1|AW076363
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|91051044|gb|EB161462.1|EB161462
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|32836424|gb|CD976102.1|CD976102
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGT
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGT
EST: gi|5901323|gb|AW042423.1|AW042423
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|8273182|gb|BE012272.1|BE012272
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|78022284|gb|DV490671.1|DV490671
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|32836575|gb|CD976253.1|CD976253
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGCACAAGACTGGCTCAGTGT
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATG-ACAAGACTGGCTCAGTGT
EST: gi|71443427|gb|DR824477.1|DR824477
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGACCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|71329430|gb|DR801431.1|DR801431
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|93283751|gb|EB676015.1|EB676015
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|86474885|gb|DY241255.1|DY241255
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|149010273|gb|EE042100.2|EE042100
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|211364468|gb|FL432340.1|FL432340
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|50335616|gb|CO530742.1|CO530742
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
EST: gi|5668501|gb|AI932016.1|AI932016
EST:     AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT                         GCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG
genomic: AGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTG

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: 43 (upstream exon), 23 (downstream exon)
Score: 4

ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTGTCGACGCACAAAACATCTCCGCTGGGTGGAGATTTCAATGGCACAACTC


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 34

ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTGTCGACGCACAAAACATCTCCGCTGGGTGGAGATTTCAATGGCACAACTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 34

ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTGTCGACGCACAAAACATCTCCGCTGGGTGGAGATTTCAATGGCACAACTC


Block sizes: 33 (upstream exon), 49 (downstream exon)
Score: 16

ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACTgtaagtttca ... tgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTGTCGACGCACAAAACATCTCCGCTGGGTGGAGATTTCAATGGCACAACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgcatgtgccatcttgatgagttaaatgccgaacttgtttctttgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTGTCGACGCACAAAACATCTCCGCTGGGTGGAGATTTCAATGGCACAACTC
             tcttgat  putative branch site (score: 16)
                                       tttctttgtgtttc  putative PPT
                     agttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcaaattcatcatagctgtcctttgccctgcaggaatctgagcctacagtatagcctaaccttgtttgtgtagttcgtgtagttcacagtgggagacgcatgtgccatcttgatgagttaaatgccgaacttgtttctttgtgtttcagGCTCCTCGAGCATTAAAATTGAGGATGACAAGACTGGCTCAGTGTACACTGTCGACGCACAAAACATCTCCGCTGGGTGGAGATTTCAATGGCACAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT