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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgtgtaaagcacagcctgcagttcagtcgtgtttttcatgaggcagatgataacaacactcttctttcactgtttgtagATGCCGTGCCACAGCAGGAACATCATGTTGTGGACCGATCACCACCTCAACCTGAGGAGGAGGAGGAGGCTGAGGTTTACGATCCGCCGCCAGAGGAAGT

Basic information

species Zea mays
transcript GRMZM2G091995_T02
intron # 3
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|71766908|gb|DR964845.1|DR964845
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|71766908|gb|DR964845.1|DR964845
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|71766908|gb|DR964845.1|DR964845
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|71768664|gb|DR966601.1|DR966601
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|71768664|gb|DR966601.1|DR966601
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|71768664|gb|DR966601.1|DR966601
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148964753|gb|EC906012.2|EC906012
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         ATGCCGTGCCACAGCAGGAACATCATGTTGTGGACCGATCACCACCTCAAC
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtagATGCCGTGCCACAGCAGGAACATCATGTTGTGGACCGATCACCACCTCAAC
EST: gi|94473274|gb|EB702232.1|EB702232
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|94473274|gb|EB702232.1|EB702232
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|94473274|gb|EB702232.1|EB702232
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211393824|gb|FK983472.1|FK983472
EST:     GCCAACGGCACATCTACTCTTGCTGTGGGAGC-TGCCACCCCTGATGACC                         G
genomic: GCCAACGGCACATCTACTCTTGCTGTGG-AGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211393824|gb|FK983472.1|FK983472
EST:     GCCAACGGCACATCTACTCTTGCTGTGGGAGC-TGCCACCCCTGATGACC                         G
genomic: GCCAACGGCACATCTACTCTTGCTGTGG-AGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211393824|gb|FK983472.1|FK983472
EST:     GCCAACGGCACATCTACTCTTGCTGTGGGAGC-TGCCACCCCTGATGACC                         G
genomic: GCCAACGGCACATCTACTCTTGCTGTGG-AGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211396446|gb|FK983487.1|FK983487
EST:     TGCCA-CGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211396446|gb|FK983487.1|FK983487
EST:     TGCCA-CGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211396446|gb|FK983487.1|FK983487
EST:     TGCCA-CGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148956890|gb|EC902811.2|EC902811
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148956890|gb|EC902811.2|EC902811
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148956890|gb|EC902811.2|EC902811
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211393820|gb|FK983468.1|FK983468
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211393820|gb|FK983468.1|FK983468
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211393820|gb|FK983468.1|FK983468
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|149047149|gb|EE048155.2|EE048155
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|149047149|gb|EE048155.2|EE048155
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|149047149|gb|EE048155.2|EE048155
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211393819|gb|FK983467.1|FK983467
EST:     TGCCA-CGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211393819|gb|FK983467.1|FK983467
EST:     TGCCA-CGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211393819|gb|FK983467.1|FK983467
EST:     TGCCA-CGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148959103|gb|EE010585.2|EE010585
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148959103|gb|EE010585.2|EE010585
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148959103|gb|EE010585.2|EE010585
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211396445|gb|FK983486.1|FK983486
EST:     TGC-AACGGCACATCTACTCTTGCTGTGGAGC-TGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211396445|gb|FK983486.1|FK983486
EST:     TGC-AACGGCACATCTACTCTTGCTGTGGAGC-TGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|211396445|gb|FK983486.1|FK983486
EST:     TGC-AACGGCACATCTACTCTTGCTGTGGAGC-TGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148957059|gb|EC903023.2|EC903023
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148957059|gb|EC903023.2|EC903023
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|148957059|gb|EC903023.2|EC903023
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|91055356|gb|EB165774.1|EB165774
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|91055356|gb|EB165774.1|EB165774
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-
EST: gi|91055356|gb|EB165774.1|EB165774
EST:     TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACC                         G
genomic: TGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtag-

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 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 35 (downstream exon)
Score: 6

ACCGCTGTAGAGGCGCAGCCAGAGGCGGATGCTGTAGTCCTGTCTGTGGCTGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtagATGCCGTGCCACAGCAGGAACATCATGTTGTGGACCGATCACCACCTCAACCTGAGGAGGAGGAGGAGGCTGAGGTTTACGATCCGCCGCCAGAGGAAGT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 9

ACCGCTGTAGAGGCGCAGCCAGAGGCGGATGCTGTAGTCCTGTCTGTGGCTGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtagATGCCGTGCCACAGCAGGAACATCATGTTGTGGACCGATCACCACCTCAACCTGAGGAGGAGGAGGAGGCTGAGGTTTACGATCCGCCGCCAGAGGAAGT


Block sizes: 48 (upstream exon), 35 (downstream exon)
Score: 11

ACCGCTGTAGAGGCGCAGCCAGAGGCGGATGCTGTAGTCCTGTCTGTGGCTGCCAACGGCACATCTACTCTTGCTGTGGAGCCTGCCACCCCTGATGACCgtagtgtgta ... ctgtttgtagATGCCGTGCCACAGCAGGAACATCATGTTGTGGACCGATCACCACCTCAACCTGAGGAGGAGGAGGAGGCTGAGGTTTACGATCCGCCGCCAGAGGAAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcgtgtttttcatgaggcagatgataacaacactcttctttcactgtttgtagATGCCGTGCCACAGCAGGAACATCATGTTGTGGACCGATCACCACCTCAACCTGAGGAGGAGGAGGAGGCTGAGGTTTACGATCCGCCGCCAGAGGAAGT
                       tgataac  putative branch site (score: 11)
                                  ctcttctttcactgtt  putative PPT
       tttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgtgtaaagcacagcctgcagttcagtcgtgtttttcatgaggcagatgataacaacactcttctttcactgtttgtagATGCCGTGCCACAGCAGGAACATCATGTTGTGGACCGATCACCACCTCAACCTGAGGAGGAGGAGGAGGCTGAGGTTTACGATCCGCCGCCAGAGGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA