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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatatgaagcaattaaaatctactgtttccctttcccccaccgccaccggatgctattcccttcaagtcccgcgactaatttccagcgacatgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTGGTACGATCTTGCGTACGGGAGGGACCATTTCTTCATCTACCTCTTCTTC

Basic information

species Zea mays
transcript GRMZM2G105631_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105631_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g09930.1 (Oryza sativa), 3'ss of exon 8
gtatatata--tgaagcaattaaaatctactgtttccctttcccccaccgccaccggatgctattcccttcaagtcccgcgactaatttccagcgacatgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTGGTACGATCTTGCGTACGGGAGGGACCATTTCTTCATCTACCTCTTCTTC
|||   | |  |||    |  |||| ||         ||||    |        | | |  |  | |  | |  ||  | ||| ||||||   |  | |  | ||||||  |||||||||||||||| ||||| || |||||||||||||| || ||||| |||||||| | ||||| ||||||||||||||||||||||||||||
gtaagaaaaattgatcagaacaaaaactctgccaaatctttataactgttttctcagctcatgattcactgatttcgagtgac-aatttcttcc--cttttttcagGCTAAACGTCACGGAGCTCGGCGTGGCGGCATTCCTCTTCTCCTGTGGATGGTATGATCTTGCATTCGGGAAGGACCATTTCTTCATCTACCTCTTCTTC
















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|60353686|gb|DN220659.1|DN220659
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
EST: gi|93284005|gb|EB676269.1|EB676269
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
EST: gi|60336764|gb|DN203737.1|DN203737
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
EST: gi|29544715|gb|CB605095.1|CB605095
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
EST: gi|78110271|gb|DV528686.1|DV528686
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
EST: gi|76292862|gb|DV032430.1|DV032430
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
EST: gi|29167909|gb|CB411169.1|CB411169
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGG
EST: gi|15427286|gb|BI543108.1|BI543108
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
EST: gi|71761578|gb|DR959515.1|DR959515
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
EST: gi|71330488|gb|DR802010.1|DR802010
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTG
EST: gi|116829022|gb|EC863362.1|EC863362
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCT
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCT
EST: gi|71298388|gb|DR785175.1|DR785175
EST:     TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAG                         GCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG
genomic: TCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTG

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: 196

CCAACGAGTGGGTGGTGACGGCGAAGCTCGGCAGCGCCATGAAGATGAAATCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTGGTACGATCTTGCGTACGGGAGGGACCATTTCTTCATCTACCTCTTCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

CCAACGAGTGGGTGGTGACGGCGAAGCTCGGCAGCGCCATGAAGATGAAATCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTGGTACGATCTTGCGTACGGGAGGGACCATTTCTTCATCTACCTCTTCTTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 96

CCAACGAGTGGGTGGTGACGGCGAAGCTCGGCAGCGCCATGAAGATGAAATCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTGGTACGATCTTGCGTACGGGAGGGACCATTTCTTCATCTACCTCTTCTTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 72

CCAACGAGTGGGTGGTGACGGCGAAGCTCGGCAGCGCCATGAAGATGAAATCGGCTAACAAAGCGGGGCTCAGGAAGCAGTTCATGAGGATATGGGAGAGgtatatatat ... catgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTGGTACGATCTTGCGTACGGGAGGGACCATTTCTTCATCTACCTCTTCTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccggatgctattcccttcaagtcccgcgactaatttccagcgacatgatgcagGCTGCACGTCACGGAGCTCGGGGTGGCAGCCTTCCTCTTCTCCTGCGGCTGGTACGATCTTGCGTACGGGAGGGACCATTTCTTCATCTACCTCTTCTTC
                             gactaat  putative branch site (score: 72)
                              actaattt  TA-rich tract