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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactaccttatgcagcaattcctgttttccccatatcttttttatatacactggataggtatccttagcatattttctgttgctgattattaattttaagtgctgaacaattctatactaaaggtgatttaaattgtcataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG

Basic information

species Zea mays
transcript GRMZM2G075101_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075101_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g64920.1 (Oryza sativa), 3'ss of exon 7
gtgactaccttatgcagcaattcctgttttc--ccca------tatcttttttatatacact-ggataggtatccttagcata------ttttctgttgctgattattaattttaagtgctgaacaattctatactaaaggtgatttaaat-tgtcataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG
|||| || ||||||||    || || |||||  ||||       ||  || |  | |||  |  ||||  |||  ||  |||       ||||||| |   | ||   |  |||| ||| |    | || ||      || ||||  || |   |   | | |||||||| ||||||||||| || |||||||| || || ||||||||||| || |||||||||||||||||| | |||||||||||||| || ||||| |||
gtgaatatcttatgcaatggtttcttttttcttcccaatttcccatacttctgctgtacgttcagataaatatttttgacatgatatctttttctgctaacggttgccatctttatgtgttttg-agttttacttgttagatgatagaattgcttttcattgtagGAAATTCATCCTTGGACACATATGATGGAGGTCCCTCAATTGCATGGTTTTGGTCCAGCTGCTAATCGCTTGTTGGAGGCATATAACACACTTTTGAAG
















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|93012884|gb|EB638404.1|EB638404
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACCCAATATATATTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|37398489|gb|CF636559.1|CF636559
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|74246322|gb|DT654236.1|DT654236
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|71761514|gb|DR959451.1|DR959451
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|32942644|gb|CF047463.1|CF047463
EST:     GTTAAATCCTTCAACACAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: GTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|6601609|gb|AW256155.1|AW256155
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACCCAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|71773508|gb|DR971408.1|DR971408
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|76020456|gb|DT947626.1|DT947626
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|37388177|gb|CF631295.1|CF631295
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|31364678|gb|CD449033.1|CD449033
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|89250411|gb|DY622197.1|DY622197
EST:     TGCAATCATTTTTGGAAACGGTTAAATCCTTCACCACAATATATACTAAG                         GAAATCCATCCTTGGACCCCCATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: TGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
EST: gi|32942426|gb|CF047245.1|CF047245
EST:     GTTAAATCCTTCAACACAATATATACTAAG                         GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC
genomic: GTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaagtgctgaacaattctatactaaaggtgatttaaattgtcataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG
                       tactaaa  putative branch site (score: 1)
                                tgatttaaattgtcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactaccttatgcagcaattcctgttttccccatatcttttttatatacactggataggtatccttagcatattttctgttgctgattattaattttaagtgctgaacaattctatactaaaggtgatttaaattgtcataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG