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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaaatactttaaaaccacaagtcactgaatggcatcagaattcagaacagcctgcaagctgttgctaaacttaacctagtagaattaccactttagttcagttcttctggactgagatatgtgctctgcaagagtgttagtaactagaagttactcctgcag

Basic information

species Zea mays
transcript GRMZM2G022866_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022866_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g44400.1 (Oryza sativa), 5'ss of exon 10
GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaaatactttaaaaccacaagtcactgaatggcatcagaattcagaacagcctgcaagctgttgctaaacttaacctagtagaattaccactttagttcagttcttctggactgagatatgtgctctgcaagagtg-ttagtaactagaagttactcctgcag
|||||||| ||||||||| ||||||||||||| ||||| || || || || |||||  |||||||||||||  ||| ||   |       ||| | | ||  ||| ||    | ||          ||   | | ||   |   | |    ||  |  |  ||| || ||   ||   | |    | ||  |    | | ||    ||||   | ||| ||  || || || | |   
GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaataacgtta------caccaatgacaaaattgct---ggatatgctgttagctatcatcagtgttttttcctgctgtaaaatcacaacc-ctgtatcacaaagccttgcaattgcaagcactacactcttggagtaactggtagctgaaaatttctgcag---

upper sequence: GRMZM2G022866_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 9
--------------------------------GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaaatactttaaaaccacaagtcactgaatggcatcagaattcagaacagcctgcaagctgttgctaaacttaacctagtagaattaccactttagttcagttcttctggactgagatatgtgctctgcaagagtg-ttagtaactagaagttactcctgcag
                                |||||||| ||||||||| ||||||||||||| ||||| || || || || |||||  |||||||||||||  ||| ||   |       ||| | | ||  ||| ||    | ||          ||   | | ||   |   | |    ||  |  |  ||| || ||   ||   | |    | ||  |    | | ||    ||||   | ||| ||  || || || | |   
CAGAATCTGACCGGTGCATGCTTTATCATCAGGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaataacgtta------caccaatgacaaaattgct---ggatatgctgttagctatcatcagtgttttttcctgctgtaaaatcacaacc-ctgtatcacaaagccttgcaattgcaagcactacactcttggagtaactggtagctgaaaatttctgcag---
















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|211302326|gb|FL459923.1|FL459923
EST:     TTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGAGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|45847020|gb|CN070963.1|CN070963
EST:     TTAGTACGAGAGACGCTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|18167421|gb|BM337260.1|BM337260
EST:     TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAG                         CTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|78076799|gb|DV505233.1|DV505233
EST:     TTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGAGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|149086438|gb|EE175981.2|EE175981
EST:     TTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGAGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|12969746|gb|BG266636.1|BG266636
EST:     TTAGTACGAGAGACGCTTGTCGAGTTGGAATTGTCACATCTGCTACACAG                         CTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|71774726|gb|DR972604.1|DR972604
EST:     TTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGAGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|5706290|gb|AI942066.1|AI942066
EST:     TTAGTACGAGAGACGCTTGTCGAGTTGGAATTGCCACATCTGCTACNCAG                         CTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT

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: 47 (upstream exon), 29 (downstream exon)
Score: 21

GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 79

GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 21

GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG