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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatcgaatatattgggttattcttgaataagtgaattcacatatttcctggtaactgctcactcatttacactatctttccacatttttgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG

Basic information

species Zea mays
transcript GRMZM2G169773_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 10
----ttgatcgaatatattgggttattcttgaataagtgaattcacatatttcctggtaactgctcactcatttacactatctttccacatttttgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG
     |    || |   |   | | | ||| | | | |  |||  ||| | || |   |     | | ||||  ||| | |     |||| |||  || | ||||||||||||||||||||||||||| ||||||||||||||||||| |||||| | |||||||| |||
gggactctgggagttcgtgatgctttgcttaatttatttgattggcatgtctcatacaattgattgagtcatcaacattgtt----cacactttctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 10
ttgatcgaatatattg-ggttattcttgaat--aagtgaattcacatatttcctggtaactgctcactcatttacactatctttccacatttttgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG
 ||    |   | |||    || |   ||||  ||   ||   | || | | ||  | | || |   || ||||   |   ||||  ||||  ||  |   |||| || |||||||||||||||||| |||||||| ||||| |  || |||||||    || ||||||
atgcctcatccttttgcaaatactacagaatgcaacctaagcaatat-tctgcttctgaatgattgatcttttattatgattttctccatt--tgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 11
ttgatcgaatatat-tgggttattcttgaataag-tgaattcacatatttcctggtaactgctc--actcatttacactatctttccacatttttgtttgcca--gATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG
       ||  ||  ||  ||   |||| || || |  |        | ||  |   |  |||   |  | |||||   ||   |  |  | ||  |||   |  ||| || ||||||||||| ||||||||||||||  |||||||| |||||||||||   || ||||||
------aaacctaggtgacttgaccttgcatgagatacacatgagggtctctagaatatcgctggaagccttttactggattgattgatttcttcttttattatagATCTTCTACTTCATTGGGTTTGGAATGTTCTGTGTTGAATCAGTGCTCAGCATCTGGGTTATTCAG

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
--ttgatcgaatat-attgggttattcttgaataagtgaattcacatatttcctggtaactgctcactcatttacactatctttccacatttt-tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG
  ||||   | ||| ||  ||  |||| ||    ||||  ||    | |||| |  |   |  |     |   |         |  ||| ||  | | |  |||||||| ||| | |||||||||||| ||||||||||||||||||||||||| |||   ||  |||||
ccttgacaaattattatcagg--attcatgg--tagtggctttttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG

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|76293307|gb|DV032875.1|DV032875
EST:     TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
genomic: TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
EST: gi|88749197|gb|DY533338.1|DY533338
EST:     TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
genomic: TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
EST: gi|76293306|gb|DV032874.1|DV032874
EST:     TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
genomic: TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
EST: gi|8368017|gb|BE050962.1|BE050962
EST:     TGGGATTTTGCCGGCTATGGATATCATAGGCAGGAGTGCTATTGTGGGG                         ATATTTTACTTCATTGTATTTGGAATGCTCTGCCTTGAATCACTGCTCAGC
genomic: TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
EST: gi|211151165|gb|FL467100.1|FL467100
EST:     TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
genomic: TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
EST: gi|78115058|gb|DV533446.1|DV533446
EST:     TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
genomic: TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
EST: gi|91049868|gb|EB160286.1|EB160286
EST:     TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGAATGTTTTGCCTTGAATCACTGCTCAGC
genomic: TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
EST: gi|78077113|gb|DV505547.1|DV505547
EST:     TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC
genomic: TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGC

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: 45 (upstream exon), 49 (downstream exon)
Score: 111

TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 313

TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 347

TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 226

TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGGgtaagtctaa ... tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctggtaactgctcactcatttacactatctttccacatttttgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG
            tgctcac  putative branch site (score: 226)
                               tctttccacattttt  putative PPT
                                        atttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatcgaatatattgggttattcttgaataagtgaattcacatatttcctggtaactgctcactcatttacactatctttccacatttttgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG

- - - - - - - - - - attcttg
- - - - - - - - - - - - - - - - - - - - - - - ttcctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -actgctc