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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatctcagaaacctgattatgtaaagtataaccctattctgtttctgactcgtcagttcctcttcaattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT

Basic information

species Zea mays
transcript GRMZM2G366935_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g40840.1 (Oryza sativa), 3'ss of exon 4
gtgagtatctcagaa-acctgattatgtaaagtataaccctattctgtttctgactcgtcagttcctcttcaattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
||||||| |||| || |  ||||     |||   ||  | | ||||||||||  |  |     || || | | |  |||||||||| || || ||  |||||||||||||||| |||||||||||||||
gtgagtacctcaaaatatttgatcccaaaaatcttagtctt-ttctgtttctctcctgatcagtcttccttactggccagCTGTGTCCAGATTCAAGGATGGTTTGACTATCGCAATCATATATGCATT
















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|148983054|gb|EE028963.2|EE028963
EST:     GAGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGATCTCT                         CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
genomic: GAGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGATCTCTgtgagtatct ... caattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
EST: gi|211042609|gb|FL405101.1|FL405101
EST:     GAGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGATCTCT                         CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
genomic: GAGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGATCTCTgtgagtatct ... caattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
EST: gi|93015243|gb|EB640763.1|EB640763
EST:     GAGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGATCTCT                         CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
genomic: GAGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGATCTCTgtgagtatct ... caattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
EST: gi|211070907|gb|FL383766.1|FL383766
EST:     AGATAGATGTGCTCAATCGCCTTGC-GCAAAATGAGAAATACAGATCTCT                         CTGTGTTCAA-TACAGAGATGGTTTGACTATCGTAATCATATATGCATT
genomic: AGATAGATGTGCTCAATCGCCTTGCAG-AAAATGAGAAATACAGATCTCTgtgagtatct ... caattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
EST: gi|149000442|gb|EE037616.2|EE037616
EST:     GAGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGATCTCT                         CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
genomic: GAGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGATCTCTgtgagtatct ... caattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
EST: gi|211340986|gb|FL379602.1|FL379602
EST:     AGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGATTCTCT                         CTGTGTTCAA-TACAGAGATGGTTTGACTATCGTAATCATATATGCATT
genomic: AGATAGATGTGCTCAATCGCCTTGCAGAAAATGAGAAATACAGAT-CTCTgtgagtatct ... caattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaagtataaccctattctgtttctgactcgtcagttcctcttcaattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT
                       ttctgac  putative branch site (score: 2)
                                     ttcctcttc  putative PPT
                                           ttcaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatctcagaaacctgattatgtaaagtataaccctattctgtttctgactcgtcagttcctcttcaattaccagCTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG