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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatgaaaaattctcaatgaaacatacaatattttgataaaaaatttatgctagtcatcaagaaaagctgctcattttgagataggcttttgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAAGTCTCACGAGTGAATGGTGAGGCACCGAATGAGCCTCCATCAACCCTTG

Basic information

species Zea mays
transcript GRMZM2G172584_T01
intron # 2
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|211208266|gb|FL105845.1|FL105845
EST:     CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAG                         ACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
genomic: CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
EST: gi|211205696|gb|FL105841.1|FL105841
EST:     CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAG                         ACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
genomic: CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
EST: gi|211208272|gb|FL105851.1|FL105851
EST:     CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAG                         ACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
genomic: CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
EST: gi|211208267|gb|FL105846.1|FL105846
EST:     CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAG                         ACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
genomic: CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
EST: gi|211208263|gb|FL105842.1|FL105842
EST:     CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAG                         ACACAAGAAGCAGCTGCTGCAGAAGA
genomic: CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGA
EST: gi|71759653|gb|DR957590.1|DR957590
EST:     CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAG                         ACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCCCAAAACGGTATGGAA
genomic: CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
EST: gi|71438774|gb|DR819824.1|DR819824
EST:     CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAG                         ACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
genomic: CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
EST: gi|211522948|gb|FK999506.1|FK999506
EST:     CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAG                         ACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
genomic: CATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAA
EST: gi|211208273|gb|FL105852.1|FL105852
EST:     ATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCA-CGAGGATCAG                         ACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGA
genomic: ATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGC-AGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGA

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: 38 (upstream exon), 41 (downstream exon)
Score: 45

CTGTACGGGAGAGATGGATGGGTGTTCCTGGAGGAGGGATCATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAAGTCTCACGAGTGAATGGTGAGGCACCGAATGAGCCTCCATCAACCCTTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 20

CTGTACGGGAGAGATGGATGGGTGTTCCTGGAGGAGGGATCATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAAGTCTCACGAGTGAATGGTGAGGCACCGAATGAGCCTCCATCAACCCTTG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 37

CTGTACGGGAGAGATGGATGGGTGTTCCTGGAGGAGGGATCATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAAGTCTCACGAGTGAATGGTGAGGCACCGAATGAGCCTCCATCAACCCTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 18

CTGTACGGGAGAGATGGATGGGTGTTCCTGGAGGAGGGATCATACAGTATCGTGCTTAAAGTCCTGGAAGAACAGGCGCAGCAGGATCAGgtgaactcac ... tgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAAGTCTCACGAGTGAATGGTGAGGCACCGAATGAGCCTCCATCAACCCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgctagtcatcaagaaaagctgctcattttgagataggcttttgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAAGTCTCACGAGTGAATGGTGAGGCACCGAATGAGCCTCCATCAACCCTTG
                                         cttttgtt  CT-rich tract
                                          ttttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatgaaaaattctcaatgaaacatacaatattttgataaaaaatttatgctagtcatcaagaaaagctgctcattttgagataggcttttgttatgcagACACAAGAAGCAGCTGCTGCAGAAGAGGCATTACCACAAAACGGTATGGAAGTCTCACGAGTGAATGGTGAGGCACCGAATGAGCCTCCATCAACCCTTG

- atgaaaaa
- - - - - - - caatgaaa
- - - - - - - - - - - catacaa
- - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - -ttatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa