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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaaaataacaaccacttctgtgtttgctcccgaatggagtcatatatttttataacatgttacatctgcagTTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTTGCAATTTGGGCTAAAGCGTATGGCAAGGTTACACATACATTTCTCAAGCGGCTTACC

Basic information

species Zea mays
transcript GRMZM2G061783_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061783_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 4
gtatgtgaaaataacaaccacttctgtgtttgctcccgaatggagtcatatatttttataacatgttacatctgcagTTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTTGCAATTTGGGCTAAAGCGTATGGCAAGGTTACACATACATTTCTCAAGCGGCTTACC
||||||||   |      | | | ||   |  || | ||||       |   ||| ||     | ||  |||  ||||||||||||||||||| ||||| || ||||| || || || |||||    |||||||| || ||||||||||||||  ||||||||||||| ||||||||
gtatgtgatttttgagttcccctttgcactctctacagaataatagtttg-gtttgtactgattcttttatccacagTTTGTGTGCATGGAACATACAGGAAGAACCTCGATTCAATCTTGCATCAGGGGCTAAAACGAATGGCAAGGTTACATGTACATTTCTCAAGTGGCTTACC

upper sequence: GRMZM2G061783_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G37310.1 (Glycine max), 3'ss of exon 7
---------------------------gtatgtgaaaataacaaccacttctgtgtttgctcccgaatggagtcatatatttttataacatgttacatctgcagTTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTTGCAATTTGGGCTAAAGCGTATGGCAAGGTTACACATACATTTCTCAAGCGGCTTACC
                            ||  |    ||        ||||||| ||        | | |  ||||||  ||    |   ||  || | | ||||||||||||||||||| |||||||| ||||| || || ||| |   || ||| || ||||| |||   || || ||  | ||||| ||  | || |||||
tgtatatctgtcttttcaagtcattctataaatttggatttttttttcttctgttttgctattttatttgtttcatatgcttg---attttgccac-tatacagTTTGTGTGCATGGAACCTACAGAAAGAACCTGGAATCAATTCTAGGATCTGGTCTGAAGCGCATGAAGAGATTGCATGTTCATTTTTCTTGTGGTTTACC
















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|148954498|gb|EC899929.2|EC899929
EST:     CACATCAGAGAGCCTGCTGAAGCCCATTTTGTCCCCCGACGAAGTGTCAG                         TTTGTGTGCATGGAACTTAC
genomic: CACATCAGAGAGCCTGCTGAAGCCCATTTTGTCCCCCGACGAAGTGTCAGgtatgtgaaa ... acatctgcagTTTGTGTGCATGGAACTTAC
EST: gi|74234857|gb|DT642771.1|DT642771
EST:     CACATCAGAGAGCCTGCTGAAGCCCATTTTGTCCCCCGACGAAGTGTCAG                         TTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTTTGCA-TTT
genomic: CACATCAGAGAGCCTGCTGAAGCCCATTTTGTCCCCCGACGAAGTGTCAGgtatgtgaaa ... acatctgcagTTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTT-GCAATTT

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), 45 (downstream exon)
Score: 46

ACTGTCACATCAGAGAGCCTGCTGAAGCCCATTTTGTCCCCCGACGAAGTGTCAGgtatgtgaaa ... acatctgcagTTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTTGCAATTTGGGCTAAAGCGTATGGCAAGGTTACACATACATTTCTCAAGCGGCTTACC


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 50

ACTGTCACATCAGAGAGCCTGCTGAAGCCCATTTTGTCCCCCGACGAAGTGTCAGgtatgtgaaa ... acatctgcagTTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTTGCAATTTGGGCTAAAGCGTATGGCAAGGTTACACATACATTTCTCAAGCGGCTTACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

ACTGTCACATCAGAGAGCCTGCTGAAGCCCATTTTGTCCCCCGACGAAGTGTCAGgtatgtgaaa ... acatctgcagTTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTTGCAATTTGGGCTAAAGCGTATGGCAAGGTTACACATACATTTCTCAAGCGGCTTACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

ACTGTCACATCAGAGAGCCTGCTGAAGCCCATTTTGTCCCCCGACGAAGTGTCAGgtatgtgaaa ... acatctgcagTTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTTGCAATTTGGGCTAAAGCGTATGGCAAGGTTACACATACATTTCTCAAGCGGCTTACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtgtttgctcccgaatggagtcatatatttttataacatgttacatctgcagTTTGTGTGCATGGAACTTACAGAAAAAACCTTGACTCGATTTTGCAATTTGGGCTAAAGCGTATGGCAAGGTTACACATACATTTCTCAAGCGGCTTACC
                                 ttataac  putative branch site (score: 50)
                         atatatttttataaca  TA-rich tract