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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACTACAGGCTAAAAAGGATCAATTGAGAATCTGGACAGGGTTCAAGCCACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtcttacattctccgatgacagtgtgtattcatcatgttcacataattgtatgatagtaactattttttttccatgttgatctcttcgcag

Basic information

species Zea mays
transcript GRMZM2G136296_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 8
AGAACTACAGGCTAAAAAGGATCAATTGAGAATCTGGACAGGGTTCAAGCCACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtcttacattctccgatgacagtgtgtattcatcatgttcacataattgtatgatagtaactattttttttccatgttgatctcttcgcag
 || || |||||||| ||||| || |||||||| |||||||| || |||||||| ||||||||||||||||| || || ||||||||||| |||||||||||| ||      |||||  | |     |||||||||        |||| ||  |  ||| | | ||| |||  ||   ||||||||  |||  ||
TGAGCTTCAGGCTAAGAAGGACCAGTTGAGAATTTGGACAGGATTTAAGCCACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAAgtgggttccctgttctcacaagta---gtgtattca--------acatgatcatgcgattgaagctaatttgcttt-gtgttgatcctttcatag

upper sequence: GRMZM2G136296_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 5'ss of exon 9
AGAACTACAGGCTAAAAAGGATCAATTGAGAATCTGGACAGGGTTCAAGCCACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtcttacattctc-cgatgacagtgtgtattc-atcatgttcacat--aattgtatgatagtaactattttttttccatgttgatctcttcgcag
|||||| || || || ||| ||| ||||||| ||||||||   |     || ||    ||||| |||||| | ||||| |||||||| ||||||||||||||| ||  |   |   |   |||     ||  || | ||| | |  | ||  |||| ||   || |   ||| |   |  ||| |||  || ||     
AGAACTTCAAGCGAAGAAGAATCGATTGAGATTCTGGACAAACTATGTTCCCCCACCCACAAATTCGAAGGCAATTCACGACCAGAATTTTACTGGAAAAgtgggtagttggtcaacataatgcttacgtaaatcctatcttttataaatggaattttaccctaatt-ttatgtccatctcat-ttggcctttttag--
















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|18384788|gb|BM417987.1|BM417987
EST:     CACCTGTGACAAACTCGAAGCCCATCCATGACCAGAAATTTACTGGAAAA                         GTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
genomic: CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
EST: gi|16746003|gb|BM032433.1|BM032433
EST:     CACCTGTGACAAACTCGAAGCCCATCCATGACCAGAAATTTACTGGAAAA                         GTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
genomic: CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
EST: gi|21390058|gb|BQ528107.1|BQ528107
EST:     CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAA                         GTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
genomic: CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
EST: gi|18385299|gb|BM418498.1|BM418498
EST:     CACCTGTGACAAACTCGAAGCCCATCCATGACCAGAAATTTACTGGAAAA                         GTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
genomic: CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
EST: gi|13150309|gb|BG320631.1|BG320631
EST:     CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAA                         GTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
genomic: CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
EST: gi|22489141|gb|BU049064.1|BU049064
EST:     CACCTGTGACAAACTCGAAGCCCATCCATGACCAGAAATTTACTGGAAAA                         GTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
genomic: CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
EST: gi|32845626|gb|CD985307.1|CD985307
EST:     CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAA                         GTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
genomic: CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
EST: gi|18384789|gb|BM417988.1|BM417988
EST:     CACCTGTGACAAACTCGAAGCCCATCCATGACCAGAAATTTACTGGAAAA                         GTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
genomic: CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
EST: gi|88758397|gb|DY542766.1|DY542766
EST:     CACCTGTGACAAACTCGAAGCCCATCCATGACCAGAAATTTACTGGAAAA                         GTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT
genomic: CACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCT

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: 46 (upstream exon), 49 (downstream exon)
Score: 233

AGAACTACAGGCTAAAAAGGATCAATTGAGAATCTGGACAGGGTTCAAGCCACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGCAGTCCTTCAGCCGAACGTCGGGTTAATCTGTCAAGCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

AGAACTACAGGCTAAAAAGGATCAATTGAGAATCTGGACAGGGTTCAAGCCACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGCAGTCCTTCAGCCGAACGTCGGGTTAATCTGTCAAGCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

AGAACTACAGGCTAAAAAGGATCAATTGAGAATCTGGACAGGGTTCAAGCCACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGCAGTCCTTCAGCCGAACGTCGGGTTAATCTGTCAAGCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 350

AGAACTACAGGCTAAAAAGGATCAATTGAGAATCTGGACAGGGTTCAAGCCACCTGTGACAAACTCGAAGCCCATTCATGACCAGAAATTTACTGGAAAAgtgtgtctta ... ctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGCAGTCCTTCAGCCGAACGTCGGGTTAATCTGTCAAGCATTA