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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctggagaaacaacttgtcatctagagcacaaatgattgtcatatactcatatctactatttgatgtggagcagtaatgcatacttcatgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG

Basic information

species Zea mays
transcript GRMZM5G813909_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 4
----gtgctggagaaacaacttgtcatctagagcacaaatgattgtcatatactcatatctactatttgatgtggagcagtaatgcatacttcatgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG
     |  ||| ||| |||||| |  |  |   ||  |     |   | || |  |  || ||||||||||||| | || | || ||||||||||| ||||||||| |||||||| || |||||||| |||||||| |||||||| || |||  ||||||||||||||||
ttctcttatggtgaatcaacttcttttgcaagccatcagc---taaaacatgccaac-tccactatttgatgtgaaacactgatacatacttcatgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAACATGGTTTTAACAAG

upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 4
gtgctggagaaacaacttgtcatct------agagcacaaatga-ttgtcatatactcatatctactatttgatgtggagcagtaatgcat-acttcatgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG-
     ||  |  |   ||||    |      |  |  ||  ||| || ||| ||  | || |||||  ||| ||    | |  || ||  | ||| | |    ||||||| || || ||||| || ||||| || ||||||||||| || ||||| || ||||||||||||||| 
-----ggtaatgctttttgttgcttctgataactgtgcatttgaattatca-atcttaatgtctacattttaata---aactttattgtgtgactacctattgtgcagaTAACTGATTTGCCCTTTTCTCTGTACTCAACTTTTGTGATTGAGGCCCGTCATGGTTTTAACAAGG

upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------gtgctggagaaacaacttgtcatctagagca-caaatgattgt-catata----------ctcatatctactatttgatgtggagcagtaatgcat-acttcatgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG
                                                                                | |   || |   || |   | | | ||  |  || | ||| ||| |           || ||||||||  ||| ||         |  ||||| ||| | |    ||||||| ||||| ||||| || ||||| || ||||||||||| || ||||| || ||||||||||| |||
gtatgcttctgacatagtaatgctgaagttttattttttggaatatttttttcttttttattactttttgggttttggcagataatgatagtgctagctttttggtgcttctgataactgtgcatttgaattatcaatctaatatctacattttaata-aactttattgtgcatgactacctattgtgcagATAACAGATTTGCCCTTTTCTCTGTACTCAACTTTTGTGATTGAGGCCCGTCATGGTTTTAATAAG

upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 4
gtgctggagaaacaacttgtcatctaga-gcacaaatgattgtcatatactcatatctactatttgatgtggagcagtaatgcatacttca--tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG
 | ||     ||    |  |||  |  | ||||     || || ||||    || |||||| ||      |   ||  | |   |  |  |  |    |||||||||| || ||||| || ||||| || ||||||||||| || ||||| || |||||||| ||||| 
ttactttttgaatggatattcacatgtatgcactgg-aatggttatatttgtat-tctact-ttaatcaagcgacaacattttgttttgtaattttcttgcagATTACTGATTTGCCATTTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA

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|211188255|gb|FL327236.1|FL327236
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAAGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|149101643|gb|EE187775.2|EE187775
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|71767568|gb|DR965505.1|DR965505
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|76293281|gb|DV032849.1|DV032849
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|71446633|gb|DR827683.1|DR827683
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|71330641|gb|DR802092.1|DR802092
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|211231531|gb|FL255915.1|FL255915
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|211231534|gb|FL255918.1|FL255918
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|211231535|gb|FL255919.1|FL255919
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|6194775|gb|AW146879.1|AW146879
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|50322421|gb|CO517547.1|CO517547
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|211023229|gb|FL319670.1|FL319670
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCG
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCG
EST: gi|211274143|gb|FL330839.1|FL330839
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|78114998|gb|DV533386.1|DV533386
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|78113447|gb|DV531839.1|DV531839
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|50334362|gb|CO529488.1|CO529488
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
EST: gi|71436743|gb|DR817793.1|DR817793
EST:     AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG                         ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA
genomic: AGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGA

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), 47 (downstream exon)
Score: 81

AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 78

AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 69

AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 110

AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtactaataa ... tgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactcatatctactatttgatgtggagcagtaatgcatacttcatgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG
               atttgat  putative branch site (score: 110)
           tactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctggagaaacaacttgtcatctagagcacaaatgattgtcatatactcatatctactatttgatgtggagcagtaatgcatacttcatgaaatgcagATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG

- gctggag
- - - - - aacaact
- - - - - - - - - - - - - -agcacaa
- - - - - - - - - - - - - - - - - atgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatac