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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgattgtagccatgctccttttgtgattcgtgtaaaaacttattatttcataaattgcagaagtaaaggcgttctagtgccaagatgcagccttgcgtaacaggctaacatgctctccttttgacaatcctatcgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCTTCCTGCACCCATTGCTGAAAGCATGCAAG

Basic information

species Zea mays
transcript GRMZM2G439297_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G439297_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g29010.1 (Oryza sativa), 3'ss of exon 10
gtaagtgattgtagccatgctccttttgtgattcgtgtaaaaacttattatttcataaattgcagaagtaaaggcgttctagtgccaagatgcagccttgcgtaacaggctaacatgctctccttttgacaatcct--atcgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCTTCCTGCACCCATTGCTGAAAGCATGCAAG
                                                 |  | |||||||    |  |  |||  | || |||   |  |    | |     |||   |    ||      ||||||| ||||||  |  |   | |||||||||||||||| || ||||  ||||| ||||| ||||||||  | || || ||||| |||||||||||||| ||||||
-----------------------------------------------gcaagtgataaattcttcacttttaggaatcct-gtgtttaactatttcatcctaaaactttcagtgat------cttttgataatcctttaatggactacagATTGGGAAAGAACATCTCTTGAAAAATCTATCAGGTTTTTCAGGGCATCGTTTCTGCAACCATTGCTGAAAGCCTGCAAG
















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|71757542|gb|DR955479.1|DR955479
EST:     CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATA                         ATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCT
genomic: CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATAgtaagtgatt ... cgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCT
EST: gi|78106588|gb|DV525006.1|DV525006
EST:     CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATA                         ATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCT
genomic: CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATAgtaagtgatt ... cgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCT
EST: gi|88748322|gb|DY532463.1|DY532463
EST:     CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATA                         ATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCT
genomic: CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATAgtaagtgatt ... cgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCT
EST: gi|30088204|gb|CB886409.1|CB886409
EST:     CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATA                         ATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCT
genomic: CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATAgtaagtgatt ... cgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCT

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: 157

CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATAgtaagtgatt ... cgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCTTCCTGCACCCATTGCTGAAAGCATGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATAgtaagtgatt ... cgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCTTCCTGCACCCATTGCTGAAAGCATGCAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 35

CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATAgtaagtgatt ... cgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCTTCCTGCACCCATTGCTGAAAGCATGCAAG


Block sizes: 37 (upstream exon), 41 (downstream exon)
Score: 7

CTTTTAGGAGAGCTGAATGCTACTGGTTTTCAGACAGATCCTGAAAATAgtaagtgatt ... cgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCTTCCTGCACCCATTGCTGAAAGCATGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccttgcgtaacaggctaacatgctctccttttgacaatcctatcgagtttcagATTGGGAAAGAACGTCCCTTGGGAAATCCATCAGTTTTTTCAGAACTTCCTTCCTGCACCCATTGCTGAAAGCATGCAAG
                                       tcctatc  CT-rich tract