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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGCTGCATTTCTCCCCCCAGTTGTTAAATCCATCCAATTCTAATTCAAATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctgctgcttctccgggagctctttgagttttgagcttacagttggcagatcggttcttccaatttaaaagatatatcttataatcgatgtgaa...

Basic information

species Zea mays
transcript GRMZM2G000052_T01
intron # 2
splice site 5'
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|91048348|gb|EB158766.1|EB158766
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|32841792|gb|CD981473.1|CD981473
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|211091703|gb|FL353095.1|FL353095
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAA
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAA
EST: gi|211080232|gb|FL307134.1|FL307134
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|23357677|gb|BU645326.1|BU645326
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGACGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|37418966|gb|CF647156.1|CF647156
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATT
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATT
EST: gi|94472196|gb|EB701154.1|EB701154
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|78023763|gb|DV492150.1|DV492150
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|91870692|gb|EB401035.1|EB401035
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|101384976|gb|EB814533.1|EB814533
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|91870632|gb|EB401004.1|EB401004
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|211529116|gb|FL350179.1|FL350179
EST:     AATAGTATTTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAA-CCACACACAC
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACAC
EST: gi|101398264|gb|EB821005.1|EB821005
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|211350009|gb|FL351959.1|FL351959
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|71764900|gb|DR962837.1|DR962837
EST:     AGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|6022142|gb|AW067070.1|AW067070
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTTATT
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCT-ATT
EST: gi|211328586|gb|FL315494.1|FL315494
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|211500012|gb|FL307528.1|FL307528
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
EST: gi|154130459|gb|EC872163.2|EC872163
EST:     AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACA                         GCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG
genomic: AATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTG

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), 47 (downstream exon)
Score: 76

TCCTGCTGCATTTCTCCCCCCAGTTGTTAAATCCATCCAATTCTAATTCAAATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTGTTATTGGTGGTGGGTTTGCTGGTCTTGCTGCTGCTGATGCTCTCAGAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 51

TCCTGCTGCATTTCTCCCCCCAGTTGTTAAATCCATCCAATTCTAATTCAAATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTGTTATTGGTGGTGGGTTTGCTGGTCTTGCTGCTGCTGATGCTCTCAGAAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 25

TCCTGCTGCATTTCTCCCCCCAGTTGTTAAATCCATCCAATTCTAATTCAAATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTGTTATTGGTGGTGGGTTTGCTGGTCTTGCTGCTGCTGATGCTCTCAGAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 232

TCCTGCTGCATTTCTCCCCCCAGTTGTTAAATCCATCCAATTCTAATTCAAATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctg ... tccatgtcagGCTCATATGGTGAAAATGCTAGGAGAAAGCCACACACACCATCTGCTATTGTTATTGGTGGTGGGTTTGCTGGTCTTGCTGCTGCTGATGCTCTCAGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGCTGCATTTCTCCCCCCAGTTGTTAAATCCATCCAATTCTAATTCAAATAGTAATTGTGAAGGAGTTCAACAGAGCTGCACAGATGGCGAACAACAgtaagtcctgctgcttctccgggagctctttgagttttgagcttacagttggcagatcggttcttccaatttaaaagatatatcttataatcgatgtgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagata