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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttaccgcgaatatcagtctctttccagataccattagacagcttttcaaaagataacacgcttaccgtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCAGCTAGCGACTCGCAAGCTGAGTCACAGATCCAAAGGATACAGACCTTGT

Basic information

species Zea mays
transcript GRMZM2G161566_T03
intron # 7
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|13237004|gb|BG355018.1|BG355018
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|5343250|gb|AI795555.1|AI795555
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|211205927|gb|FL457759.1|FL457759
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|24934599|gb|CA452817.1|CA452817
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|37392587|gb|CF633545.1|CF633545
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|30087805|gb|CB886011.1|CB886011
EST:     AAAGAAAAAACGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|32164833|gb|CD670151.1|CD670151
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|32928190|gb|CF033002.1|CF033002
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|60400163|gb|DN232970.1|DN232970
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|56461974|gb|CK986272.1|CK986272
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|211413645|gb|FL414540.1|FL414540
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|37398941|gb|CF636791.1|CF636791
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|211307747|gb|FL198214.1|FL198214
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|60342476|gb|DN209449.1|DN209449
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|16378271|gb|BI992362.1|BI992362
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|60395600|gb|DN228470.1|DN228470
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|44900819|gb|CK827364.1|CK827364
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|60394746|gb|DN227616.1|DN227616
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
EST: gi|60355769|gb|DN222742.1|DN222742
EST:     AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG                         TCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA
genomic: AAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAGgtaagcttac ... gtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagataccattagacagcttttcaaaagataacacgcttaccgtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCAGCTAGCGACTCGCAAGCTGAGTCACAGATCCAAAGGATACAGACCTTGT
                                     cgcttac  putative branch site (score: 3)
                                           ccgtcttc  CT-rich tract
                     ttttcaaaagataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttaccgcgaatatcagtctctttccagataccattagacagcttttcaaaagataacacgcttaccgtcttcgcagTCACTTCATAAGATCGAGAGTTTCGTCATCGAGCACGCTGCTGATAATCCAGCTAGCGACTCGCAAGCTGAGTCACAGATCCAAAGGATACAGACCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA