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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacggctagaggcccttttgcatcacgaagatagaactaactgttatgatatccttatactctgtgcagaccataacttccttgttgttgctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG

Basic information

species Zea mays
transcript GRMZM2G086484_T01
intron # 5
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|31352814|gb|CD437171.1|CD437171
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|19770206|gb|BQ034927.1|BQ034927
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|31351667|gb|CD436024.1|CD436024
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|71762836|gb|DR960773.1|DR960773
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|71311912|gb|DR792439.1|DR792439
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|33091533|gb|CF051527.1|CF051527
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAATCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|40334296|gb|CK368366.1|CK368366
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCATCCCAG                         GAAACCAAAATACTTCTGAAGCTTCAGCTGATGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|71315320|gb|DR794272.1|DR794272
EST:     TCAATGAATCACCAATCAGTCCTCCCAG                         GAAACAAAAATATTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: TCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatatccttatactctgtgcagaccataacttccttgttgttgctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
                          ccataac  putative branch site (score: 3)
                                           ttgcttt  putative PPT
          ttatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacggctagaggcccttttgcatcacgaagatagaactaactgttatgatatccttatactctgtgcagaccataacttccttgttgttgctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG