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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgatgtcactactattttttgtctttgaattgatgtttaatgttataaatgttcagaatataccagtaaatttgcatactcatttgtttcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGCTACTGCAGTTGTTGTTAACAAAAGGAGAAGGAATATGCTTAAAGAGTTG

Basic information

species Zea mays
transcript GRMZM2G038313_T01
intron # 3
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|71333152|gb|DR803610.1|DR803610
EST:     AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAAGACAG                         GTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGC
genomic: AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGC
EST: gi|67042197|gb|CO468452.1|CO468452
EST:     AACCATGAAA-TGGTAGAAATGGGATCATTGATCTGNTCTTCCAGGACAG                         GTACTTGAATGCTATACAGACAANTGCTCACCATCTTCTGAGATAC-TAGC
genomic: AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGC
EST: gi|149075427|gb|EE163945.2|EE163945
EST:     TACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAG                         GTACTTGAATGCTATAC
genomic: AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATAC
EST: gi|71438188|gb|DR819238.1|DR819238
EST:     AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAG                         GTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGC
genomic: AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGC
EST: gi|148996096|gb|EE035357.2|EE035357
EST:     AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAG                         GTACTTGAATGCTATACAGACAAATGCT
genomic: AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATGCT
EST: gi|71429761|gb|DR810811.1|DR810811
EST:     A-CCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTC-AGGACAG                         GTACTTGAATGCTATACAGACAAATG
genomic: AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATG
EST: gi|71318808|gb|DR796165.1|DR796165
EST:     AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAG                         GTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGC
genomic: AACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGC

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), 47 (downstream exon)
Score: 358

AGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGCTACTGCAGTTGTTGTTAACAAAAGGAGAAGGAATATGCTTAAAGAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

AGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGCTACTGCAGTTGTTGTTAACAAAAGGAGAAGGAATATGCTTAAAGAGTTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 181

AGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGCTACTGCAGTTGTTGTTAACAAAAGGAGAAGGAATATGCTTAAAGAGTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 206

AGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCATTGATCTGTTCTTCCAGGACAGgtttgtctgt ... tcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGCTACTGCAGTTGTTGTTAACAAAAGGAGAAGGAATATGCTTAAAGAGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataaatgttcagaatataccagtaaatttgcatactcatttgtttcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGCTACTGCAGTTGTTGTTAACAAAAGGAGAAGGAATATGCTTAAAGAGTTG
                                   ctcatttgtttccctt  CT-rich tract
                     agtaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgatgtcactactattttttgtctttgaattgatgtttaatgttataaatgttcagaatataccagtaaatttgcatactcatttgtttcccttgcagGTACTTGAATGCTATACAGACAAATGCTCACCATCTTCTGAGATACCTAGCTACTGCAGTTGTTGTTAACAAAAGGAGAAGGAATATGCTTAAAGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
-atgatgt
- - - - - - - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgcat