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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttctatcattcatcggtctgtgctgtgtggcattagtctttgttgacatgtctaatgtatatttgtctctttcttttgttatttgttcttatattgcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG

Basic information

species Zea mays
transcript GRMZM5G871572_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 6
gtattatttctatcattcatcggtctgtgctgtgtggcattagtctttgttgacatgtctaatgtatatttgtctctttcttttgttatttgttcttatattgcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG
   | |||  || | || ||  |||||   ||  | |  || ||      |    | ||   |  ||   |   |||| |||| ||| ||  ||||||| ||| ||||| |||| |||||||||||||||||||||||| ||||||||||||| || |||||||| || |||||||| || |||||||||||||||||||| ||||||||||
--gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctat----tttcctttacatggctaagtcttgctttcgtttttgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG

upper sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G02920.1 (Glycine max), 3'ss of exon 6
gtattatttctatcattcatcggtctgtgctgtgtggcattagtctttgttgacatgtctaatgtatatttgtctc--tttcttttgtta--tttgttcttatattgcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG
            ||| | |||   || ||  |||     || || |   || | || |  |   | || |  | ||   || |||| |||  ||  || ||| | || || | ||||||  |||||||||||||||  ||||| ||||||||||||| || ||||| || || ||||| || || ||||  || |||||||| |||   ||||| |
------------tcaattatcaa-ctctg--gtgccatttttgtgtcaattaa-atattaatcctttactgttttcaacttttttttttaatttcatttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGCGCTATTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG

upper sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0104g00630.t01 (Vitis vinifera), 3'ss of exon 6
gtattatttctatcattcatcggtctgtgctgtgtggcat-tagtctttgttgacatgtctaatgtatatttgtctctttcttttgttatttgttcttatattgcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG
         ||   ||     | ||| |    |    ||  |||| ||  |||| ||  |   | | | ||||    | |  |    ||  ||||  | || |  |||| |||||||| ||||||||||||||||| ||| | |||||||| || ||||||||||| || ||||| || || ||||| || ||||| ||| ||   |||||||
---------cttgtatgaggagatctatatgattgatcaggtagttttgattga-ataccccttttttttttgcaaatcttat---atacgtgtttctttaatatatgatcagGCTATCAAAGATGATGTTGGAACAATTCGTATTCAGCGGCCCCATAAAGGACCATTTTATGTCTCTCCCAAAAGTATTGATCATCTTGTTGCAAATCTTG

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|78114655|gb|DV533043.1|DV533043
EST:     GAACTGAAAGGGTTCTTCCCACTGGAATCTCCTTGACAGTTGTTGGTGAG                         GCTATTACAGATGATGTTGGAACTATTAG
genomic: GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAG
EST: gi|93012428|gb|EB637948.1|EB637948
EST:     GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG                         GCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA
genomic: GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA
EST: gi|211009140|gb|FL186793.1|FL186793
EST:     GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG                         GCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA
genomic: GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA
EST: gi|56691676|gb|CX129579.1|CX129579
EST:     GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTGGGTGAG                         GCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA
genomic: GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA
EST: gi|149055712|gb|EE156420.2|EE156420
EST:     GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG                         GCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA
genomic: GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA
EST: gi|71432571|gb|DR813621.1|DR813621
EST:     GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG                         GCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA
genomic: GAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGA

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), 49 (downstream exon)
Score: 165

ATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 103

ATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 102

ATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

ATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAGgtattatttc ... gcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaatgtatatttgtctctttcttttgttatttgttcttatattgcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG
 gtctaat  putative branch site (score: 156)
                       ttttgttatttgttct  TA-rich tract