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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgctagataatatggacagatagtataaataatgcttattggttacagaaattccatgcatgtttcagctaatgataaattactgggacatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG

Basic information

species Zea mays
transcript GRMZM2G131756_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131756_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g37410.1 (Oryza sativa), 3'ss of exon 17
ttttgctagataatatggacagatag-tata-aataatgc-ttattggttacagaaattccatgcatgtttcagctaatgataaattactgggacatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG
    |      || | |||| | |   |||  ||| |||| || ||||||   ||| || || | ||   |   |||||||    ||||||| ||||||| |||||||||| |||||||| ||||| |||||||| |||||||||||||||||||||||||| ||||||
--cagtattgcaaaacggactgtttcctatgtaatcatgcattgttggtttgtgaagttgcaagtattgcttgactaatgacgg-ttactggaacatgaacagGTTCCTTGCCGAACAGCCATGAGAGGTAGTTTTCCACTTAATGGCACTTACTTTCAAGTTAATGAG

upper sequence: GRMZM2G131756_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g37350.1 (Oryza sativa), 3'ss of exon 16
ttttgctagataatatggacagatag-tata-aataatgc-ttattggttacagaaattccatgcatgtttcagctaatgataaattactgggacatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG
    |      || |  ||| | |   |||| ||| |||| || ||||||   ||| || || | ||   |   |||||||    ||||||| ||||||| |||||||||| |||||||| ||||| |||||||| |||||||||||||||||||||||||| ||||||
--cagtattgcaaaacagactgtttcctatacaatcatgcattgttggtttgtgaagttgcaagtattgcttgactaatgacgg-ttactggaacatgaacagGTTCCTTGCCGAACAGCCATGAGAGGTAGTTTTCCACTTAATGGCACTTACTTTCAAGTTAATGAG
















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|211540330|gb|FL320588.1|FL320588
EST:     GTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTG                         GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAACGGCACTTAC
genomic: GTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTGgtaatggaat ... acatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTAC
EST: gi|211151599|gb|FL276380.1|FL276380
EST:     AAACCAATCTAGATATGTCAGAGGCACAATTCTG                         GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTAC
genomic: AAACCAATCTAGATATGTCAGAGGCACAATTCTGgtaatggaat ... acatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTAC
EST: gi|60339031|gb|DN206004.1|DN206004
EST:     GTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTG                         GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAACGGCACTTAC
genomic: GTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTGgtaatggaat ... acatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTAC
EST: gi|60347567|gb|DN214540.1|DN214540
EST:     GTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTG                         GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTAC
genomic: GTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTGgtaatggaat ... acatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTAC
EST: gi|5901234|gb|AW042334.1|AW042334
EST:     GTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTG                         GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTAC
genomic: GTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTGgtaatggaat ... acatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTAC

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: 324

TGACCCTCAAATGGGAGGCGATTTATGCAATAATGAAATGTGCCACAATTGTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTGgtaatggaat ... acatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 37

TGACCCTCAAATGGGAGGCGATTTATGCAATAATGAAATGTGCCACAATTGTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTGgtaatggaat ... acatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 42

TGACCCTCAAATGGGAGGCGATTTATGCAATAATGAAATGTGCCACAATTGTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTGgtaatggaat ... acatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 84

TGACCCTCAAATGGGAGGCGATTTATGCAATAATGAAATGTGCCACAATTGTACTGCAGAGAAAGAAAACCAATCTAGATATGTCAGAGGCACAATTCTGgtaatggaat ... acatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacagaaattccatgcatgtttcagctaatgataaattactgggacatgaatagGTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG
                        agctaat  putative branch site (score: 84)
                           taatgataaattact  TA-rich tract