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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctttgcttttgatttttacaaacagtcaatcttattatttgtttggctataaattcgtgctatagtggtttgattgtatgtttgaactctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTG

Basic information

species Zea mays
transcript GRMZM2G178294_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178294_T04 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g11200.1 (Oryza sativa), 3'ss of exon 12
atctttgcttttgatttttacaaacagtcaatcttattatttgtttggctataaattcgtgcta--tagtggtttgattgtatgtttgaactcttt---ttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTG
 ||| |||| |    | | ||    | |  ||||   | ||||||    |||   ||    |||  |  || |  ||||| |   || | || |||   ||  ||||  | |||||||| |||||||||||||||||||||||||||||||| ||  ||||||||||||||||||| || || || ||||||||||||||| | |
gtctctgctgtaatctgtcacttgtact--atctc--tctttgttatagtatttcttttaactatttgttgatgcgattg-actcttaacctgtttgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCG
















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|32930152|gb|CF034964.1|CF034964
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|32933149|gb|CF037961.1|CF037961
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|32935217|gb|CF040029.1|CF040029
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|211488019|gb|FL401529.1|FL401529
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCAT
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCAT
EST: gi|60350628|gb|DN217601.1|DN217601
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|166645093|gb|EG281141.1|EG281141
EST:     TCTTATGCACAGCAG                         GCTGCAATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCA
genomic: TCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGC-ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCA
EST: gi|211371062|gb|FL377775.1|FL377775
EST:     CAACTTCTGAAGCATCTGGGCAACAATGSGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGG
EST: gi|32933726|gb|CF038538.1|CF038538
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGGACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|9731923|gb|BE510675.1|BE510675
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATA
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATA
EST: gi|74245848|gb|DT653762.1|DT653762
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|166462298|gb|EG185916.1|EG185916
EST:     CTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|60396359|gb|DN229228.1|DN229228
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|88747463|gb|DY531604.1|DY531604
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTTTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|211281773|gb|FL006153.1|FL006153
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|44901202|gb|CK827747.1|CK827747
EST:     CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: CAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|166481585|gb|EG161613.1|EG161613
EST:     TCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: TCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
EST: gi|211420309|gb|FL467594.1|FL467594
EST:     TGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAG                         GCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG
genomic: TGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 204

GTCAGCCACGGGAACTGATCCAAATGCTTCCAATCCTCCTGTTTGGCCTGCAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

GTCAGCCACGGGAACTGATCCAAATGCTTCCAATCCTCCTGTTTGGCCTGCAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GTCAGCCACGGGAACTGATCCAAATGCTTCCAATCCTCCTGTTTGGCCTGCAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 88

GTCAGCCACGGGAACTGATCCAAATGCTTCCAATCCTCCTGTTTGGCCTGCAACTTCTGAAGCATCTGGGCAACAATGGGGAGCTTCTTATGCACAGCAGgtcatacatt ... ctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggctataaattcgtgctatagtggtttgattgtatgtttgaactctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTG
                        gtttgat  putative branch site (score: 88)
                                           ctcttttttt  putative PPT
                                            tcttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctttgcttttgatttttacaaacagtcaatcttattatttgtttggctataaattcgtgctatagtggtttgattgtatgtttgaactctttttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- -tttgctt
- - - - - - - - - -acaaaca
- - - - - - - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcgtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtttg