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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttcagtctcattgattcattgatcgctgagcacataccatttctgtttttggtagtcatgccttgtgttctctggctacagGAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATAATTGTGACAACAATAGGAGGTCATAATGGGAAGCCAAAGCAG

Basic information

species Zea mays
transcript GRMZM2G109624_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 2
gttatttcagtctcatt-gattcattgatcgctgagcacataccatttctgtttttggtagtcatgccttgtgttctctggctacagGAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATAATTGTGACAACAATAGGAGGTCATAATGGGAAGCCAAAGCAG
|||||||   |  |||| || |  |   |   |||    || |||   ||  ||| | || | ||| | |   || ||||  || |||||  ||||||||||| | || |||  |||||| | || ||||| ||||| ||||||||| |||| |||||||| ||||||||||||||||||
gttattttgataccatttgacttgtcacttcttgacataatgccacc-ctactttcgttacttatgtcgtagtttttctgattatagGAATCTGAAGGTGTTATTGTTAATGCAAATGGAACAGAAACAGGTCAGATTATTGTGACATCAATTGGAGGTCAAAATGGGAAGCCAAAGCAG
















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|149078651|gb|EE167439.2|EE167439
EST:     TGAATGATATGACAATTAGTGACGATAAAGCTGATGACCATAATGATAAG                         GAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATA
genomic: TGAATGATATGACAATTAGTGACGATAAAGCTGATGACCATAATGATAAGgttatttcag ... ctggctacagGAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATA
EST: gi|31364485|gb|CD448840.1|CD448840
EST:     TGAATGATATGACAATTAGTGACGATAAAGCTGATGACCATAATGATAAG                         GAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATA
genomic: TGAATGATATGACAATTAGTGACGATAAAGCTGATGACCATAATGATAAGgttatttcag ... ctggctacagGAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATA

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: 386

GAAGCCTGTTAAAACTGAAGAACCAGTAGCAGATCTTCTTCCCAAAGAATTGAATGATATGACAATTAGTGACGATAAAGCTGATGACCATAATGATAAGgttatttcag ... ctggctacagGAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATAATTGTGACAACAATAGGAGGTCATAATGGGAAGCCAAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

GAAGCCTGTTAAAACTGAAGAACCAGTAGCAGATCTTCTTCCCAAAGAATTGAATGATATGACAATTAGTGACGATAAAGCTGATGACCATAATGATAAGgttatttcag ... ctggctacagGAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATAATTGTGACAACAATAGGAGGTCATAATGGGAAGCCAAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GAAGCCTGTTAAAACTGAAGAACCAGTAGCAGATCTTCTTCCCAAAGAATTGAATGATATGACAATTAGTGACGATAAAGCTGATGACCATAATGATAAGgttatttcag ... ctggctacagGAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATAATTGTGACAACAATAGGAGGTCATAATGGGAAGCCAAAGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

GAAGCCTGTTAAAACTGAAGAACCAGTAGCAGATCTTCTTCCCAAAGAATTGAATGATATGACAATTAGTGACGATAAAGCTGATGACCATAATGATAAGgttatttcag ... ctggctacagGAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATAATTGTGACAACAATAGGAGGTCATAATGGGAAGCCAAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagcacataccatttctgtttttggtagtcatgccttgtgttctctggctacagGAAGGTGAAGGTGTTACTCTTGATGGGAATGGAGCCGAGACAGGACAGATAATTGTGACAACAATAGGAGGTCATAATGGGAAGCCAAAGCAG
                                       tgttctct  CT-rich tract
                 tgttttt  TA-rich tract