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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgtttgcagcgaattctcatctgctttgaacctgctatcagatttttacatgtcattgcttgagcatctataggaggctcttctttacaataggccatgtaaaattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG

Basic information

species Zea mays
transcript GRMZM2G063492_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 13
gtgatgtttgcagcgaattctcatctgctttgaacctgctatcagatttttacatgtcattgcttgagcatctataggaggctcttctttacaataggccatgtaaaattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG
||||||||||    |  |   |  |  || ||||  || | |   |    |||    ||||  || |    ||| |      |||  | |  ||  |  |  |||||| ||||||||| || ||||||||||| |||||| ||||| |||||||||||||||||||||||||||| ||||||||||| ||||||||||||
gtgatgtttg--atggttaacctgcctctctgaaagtgatttggaaccactacca--cattaattta----ctaaaacctagtctgatatgtaac-gttctcgtaaaactttgcagTTCACCGCATCTGGTCATACTGAATTGCGAATCAATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATG

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 12
gtgatgtttgcagcgaattctcatctgctttgaacctgctatcagatttttacatgtcattgcttgagcatctataggaggctcttctttacaatag-gccatgtaaaattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG
                            |  || |    | |  |   | |  |   | | |  |       ||  |   | | ||  | | |||    |  ||||||||   |||||| ||    || |||||||||||| |||||  |||||| |||||||||||||||||  ||| |||||| ||  |||||||||||
---------------------------gtaagagcaacatgtgggggctgtttaaaacctcggatacaatcttaaggtttgatgtttctaaaaatgacactttgtaaaat---gcagTTCACCTTGTCCGGTCACACTGAACTGCGAACCAATGCCATCATGATCACCAGCACCATTACTGTTGTGCTTGTCAGCACAATG

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 12
gtgatgtttgcagcgaattctcatctgctttgaacctgctatcagatttttacatgtcattgcttgagcatctataggaggctcttctttacaataggccatgtaaaattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG
       |   ||| |  | |    ||  | |   ||| |   | |   |   ||   || |  |||   |  |||         | | || ||  | |  | |   |   ||||||| ||    || ||||||||||||  ||||  |||||| |||||||||||||||||  ||| |||||| ||  |||||||||||
------gtaagagcaacatgtggcatg--tgggggctgtt--taaaacctcggatacaatcg--tgaagtttgata---------tttctaaaagtgacactcttgtaaaatgcagTTCACCTTGTCGGGTCACACTGAACAGCGAACCAATGCCATCATGATCACCAGCACCATTACTGTTGTGCTTGTCAGCACAATG

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|18964172|gb|BM660852.1|BM660852
EST:     GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAG                         TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
genomic: GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
EST: gi|37397420|gb|CF636007.1|CF636007
EST:     GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAG                         TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
genomic: GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
EST: gi|71311178|gb|DR791899.1|DR791899
EST:     GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAG                         TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
genomic: GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
EST: gi|89106454|gb|DY576671.1|DY576671
EST:     GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAG                         TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
genomic: GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
EST: gi|78078432|gb|DV506846.1|DV506846
EST:     CAATTGCGCTTGCCTATAACAAG                         TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
genomic: CAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
EST: gi|18963602|gb|BM660527.1|BM660527
EST:     GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAG                         TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
genomic: GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
EST: gi|91872697|gb|EB402654.1|EB402654
EST:     GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAG                         TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC
genomic: GGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACC

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: 70

GTAATCATATGGTGGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 197

GTAATCATATGGTGGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 112

GTAATCATATGGTGGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

GTAATCATATGGTGGGCTGGTCTCATGAGAGGAGCAGTGTCAATTGCGCTTGCCTATAACAAGgtgatgtttg ... aattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgagcatctataggaggctcttctttacaataggccatgtaaaattttgcagTTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG
                                       atgtaaaatttt  TA-rich tract