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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcataactatgaattgttgttgtaccaaatggttatttcattattaaactgacaaaaatgccattttttagtatcaacttatctttgctttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG

Basic information

species Zea mays
transcript GRMZM2G381933_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381933_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g15490.3 (Oryza sativa), 3'ss of exon 10
ttgcataactatgaattgttgttgtac--caaatggttatttcatta-ttaaactga------caaaaatgccattttttagtatcaacttatctttgctttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG
            ||| ||||||  |||   ||||||||  ||||| | ||  |||||      || |||||||||||  |  |||||||  || |||  ||||||||  | ||||||||||||||||| |||||||| |||||||||||||| || ||| |||||||||||||||| |||||||||
------------gaactgttgtcatacactaaatggttgcttcatgaatttgactgaacaaatcacaaatgccatttactgttatcaac--atgtttaatttgaattttcatagGCTCCTGATGAAGAGTTTGAAGAATACCTTAGTCAACTGATAGGAGACAATTACACTGGTGATCGAAATGAG

upper sequence: GRMZM2G381933_T04 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA03G34140.1 (Glycine max), 3'ss of exon 10
ttgcataactatgaattgttgttgtaccaaatggttatttcattat-taaactgacaaaaatgccattttttagtatcaacttatctttgctttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG
  ||||  | ||   |   |||| |  ||  |  || |  | || | | | ||  |   |||     | | ||  || |   | | ||   || |  ||   ||||||||||||||||||||||||||| || || || ||  | || ||  |  | |  ||||||||||||||||||
--gcatctcaatttctctctgttatttcagctttttttcactttttctcatcttcctggaat----ctctatatcattattgtttgttgatttggttttgatgtagGCTCCTGATGAAGAATTTGAAGAATATCTCAGGCATATTATTGGTGATCAGTGTACTGGTGACCGAAATGAG

upper sequence: GRMZM2G381933_T04 (Zea mays), 3'ss of exon 10
lower sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 11
--------ttgcataacta--tgaattgttgttgtaccaaatggttatttcattattaaactgacaaaaatgccattttttagtatcaacttatctttgctttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG
         | || |||||    |  |  || | | | | || |  || |||  |||  |    ||  ||     |||  |    ||||       |||  || ||||    ||||| |||||||||||||||||||| || ||||| || || || ||  || ||| |||||||||||| ||||||
aaaaagagattcaaaactagtcaagcttctgctttgctacataggcatatca--attggat--gcactaactatgtttgatttggtcaa-------ttgtcttaaatt----tagGCCCCTGATGAAGAATTTGAAGAATATCTTAGGCATCTTATAGGTGACCATTGCACTGGTGACCGGAATGAG

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|71767360|gb|DR965297.1|DR965297
EST:     ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCG--T-                         C-T-GGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
genomic: ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
EST: gi|33285569|gb|CF075364.1|CF075364
EST:     ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTG                         -G----CTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
genomic: ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
EST: gi|78087486|gb|DV515879.1|DV515879
EST:     ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTG                         -G----CTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
genomic: ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
EST: gi|8516501|gb|BE123226.1|BE123226
EST:     ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCG--T-                         C-T-GGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
genomic: ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
EST: gi|67023704|gb|CO452453.1|CO452453
EST:     ATTCAGACGTTTCTTTGGCTGGTGTTGCGAAAGCATTTGGAGTTCGTCTG                         -G----CTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
genomic: ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
EST: gi|33285805|gb|CF075600.1|CF075600
EST:     ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCG--T-                         C-T-GGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
genomic: ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
EST: gi|211076372|gb|FL154532.1|FL154532
EST:     ATTCAGACGTTTCTTTGGCTGGTGTTGCGAAAGCATTTGGAGTTCG--T-                         C-T-GGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
genomic: ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
EST: gi|71767359|gb|DR965296.1|DR965296
EST:     AAGCATTTGGAGTTCG--T-                         C-T-GGCTCCTGATGAAGAATTTGAAGATTACTTTAGTCATCTCATGGGAA
genomic: AAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
EST: gi|33097429|gb|CF057389.1|CF057389
EST:     ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCG--T-                         C-T-GGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA
genomic: ATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAA

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 2 RNA-Seq libraries.


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 6

GTGTTTATTTTTGGTGGACTCGGGCCGCTACATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG


Block sizes: 29 (upstream exon), 21 (downstream exon)
Score: 1

GTGTTTATTTTTGGTGGACTCGGGCCGCTACATTCAGACGTTTCTTTGGCTGGTGTCGCGAAAGCATTTGGAGTTCGTCTGgtgcgtccaa ... tttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaactgacaaaaatgccattttttagtatcaacttatctttgctttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG
   aactgac  putative branch site (score: 1)
                                  cttatctttgcttt  putative PPT
                   attttttagtatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcataactatgaattgttgttgtaccaaatggttatttcattattaaactgacaaaaatgccattttttagtatcaacttatctttgctttgaattagCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG

-tgcataa
- - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - -tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - -acaaaaa