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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_T03
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

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: 47 (upstream exon), 46 (downstream exon)
Score: 211

TAATCCAAATGAAGACTATGCGGAGACAGAGTTGAAGTTGAGGGAATACTTGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 101

TAATCCAAATGAAGACTATGCGGAGACAGAGTTGAAGTTGAGGGAATACTTGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 99

TAATCCAAATGAAGACTATGCGGAGACAGAGTTGAAGTTGAGGGAATACTTGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 135

TAATCCAAATGAAGACTATGCGGAGACAGAGTTGAAGTTGAGGGAATACTTGCAATCATTTTTGGAAACGGTTAAATCCTTCAACACAATATATACTAAGgtgactacct ... cataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaagtgctgaacaattctatactaaaggtgatttaaattgtcataatatagGAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG
                       tactaaa  putative branch site (score: 135)
                                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