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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCTGGGAAAGCAAGTTGCTGCATCCGGTATATCAGTCTGGAACCCAGCTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctctccccttctcgaatgtttctttatatgatcagcaattttgcagagaacattgttgatatgttttgggctgactaggggttttttgattgatttgtag

Basic information

species Zea mays
transcript GRMZM2G139533_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139533_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g11050.1 (Oryza sativa), 5'ss of exon 9
TGGTCTGGGAAAGCAAGTTGCTGCATCCGGTATATCAGTCTGGAACCCAGCTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtat-cttctctccccttctcgaatg--tttctttatatgatcag--caattttgcagagaacattgttgatatgttttgggctgactaggggttttttgattgatttgtag
||| || || |||||||| || || || |||||||| || |||||||| || |||||||||||||| ||||||||||| || ||||||||||| |||||||||| |   |   || || | |  ||   |||  |  || ||  |   |  | |    |||||||||||  |||         |||| || | ||| ||| || || |  ||
TGGCCTAGGTAAGCAAGTCGCCGCGTCAGGTATATCGGTGTGGAACCCTGCCTTCGATGTTACTCCGGCAAATCTGATTACCGCAATCATAACGGAAAAGgtatacaaatgagccattgtggcgtgaacttcagttaataattggtctatatgtatgaagaacattgtttttat---------tgaccagagttttcttg-ttcatgtacag

upper sequence: GRMZM2G139533_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv11s0016g00830.t01 (Vitis vinifera), 5'ss of exon 9
TGGTCTGGGAAAGCAAGTTGCTGCATCCGGTATATCAGTCTGGAACCCAGCTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctctccccttctcgaatgtttctttatatgatcagcaatt-ttgcagagaacattgttgatatgttttgggctgactaggggttttttgattgatttgtag
 || || ||  | || ||||||||||| || || |  || |||||||| |||||||||||||| |||||  |||||||  |||  ||||||||||| |||||  ||| ||||||  | ||     ||   ||  |  |   | | || |||||    ||||  |||| ||  | ||  | |                           
AGGACTCGGGGAACAGGTTGCTGCATCTGGAATTTGTGTTTGGAACCCTGCTTTCGATGTTACCCCAGCTGATCTGATAGCTGGTATCATAACAGAGAAGgt-ccttgtctccctctttct----ttctattgcaaaacatgtatttattgcatctgacatacttga-attatatgatcag---------------------------
















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|76285910|gb|DV025478.1|DV025478
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|76017068|gb|DT944238.1|DT944238
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|88756661|gb|DY540802.1|DY540802
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|60359093|gb|DN226066.1|DN226066
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|161585418|gb|EY951935.1|EY951935
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCAACAAAAACTGA
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCA-CAAAAACTGA
EST: gi|37398320|gb|CF636472.1|CF636472
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|71445094|gb|DR826144.1|DR826144
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|211030875|gb|FL442918.1|FL442918
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|60352019|gb|DN218992.1|DN218992
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|211279443|gb|FK979043.1|FK979043
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|78180539|gb|DV551032.1|DV551032
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|67021902|gb|CO450651.1|CO450651
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|211506055|gb|FL476284.1|FL476284
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|88749182|gb|DY533323.1|DY533323
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|88756069|gb|DY540210.1|DY540210
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGGGTGATCACAAAAACTGATGCTGATGGATCTTTTGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|211470410|gb|FL454226.1|FL454226
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|71756819|gb|DR954756.1|DR954756
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|60401518|gb|DN234325.1|DN234325
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|74233419|gb|DT641333.1|DT641333
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCACAACAGAAAAG                         GGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|84969742|gb|DW468170.1|DW468170
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGGGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
EST: gi|50324231|gb|CO519357.1|CO519357
EST:     CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAG                         GGTGTGATCCCAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC
genomic: CTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTC

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), 48 (downstream exon)
Score: 141

TGGTCTGGGAAAGCAAGTTGCTGCATCCGGTATATCAGTCTGGAACCCAGCTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTCCTTCTGCCCGCAAAATAATACTCTAGCGTGGCTTCCATTCTGAATGACA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 147

TGGTCTGGGAAAGCAAGTTGCTGCATCCGGTATATCAGTCTGGAACCCAGCTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTCCTTCTGCCCGCAAAATAATACTCTAGCGTGGCTTCCATTCTGAATGACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 202

TGGTCTGGGAAAGCAAGTTGCTGCATCCGGTATATCAGTCTGGAACCCAGCTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTCCTTCTGCCCGCAAAATAATACTCTAGCGTGGCTTCCATTCTGAATGACA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 130

TGGTCTGGGAAAGCAAGTTGCTGCATCCGGTATATCAGTCTGGAACCCAGCTTTCGATGTTACTCCAGCAAATCTGATCACTGCAATCATAACAGAAAAGgtatcttctc ... tgatttgtagGGTGTGATCACAAAAACTGATGCTGATGGATCTTTCGACATCAAAGGATTCCTTCTGCCCGCAAAATAATACTCTAGCGTGGCTTCCATTCTGAATGACA