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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcccgtaggttgcagtatcgtgtttgggaaaaaaaaatgatacaatggcgatgtgcctgaatttggagtgctgacatggtaatatgcgctcttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACTGTTGGCTTGGTCTGTGAAAATTACAGCGGTCTGTTCAGACGACCCCGTG

Basic information

species Zea mays
transcript GRMZM2G085747_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 3
gtgagcccgtaggttgcagtatcgtgtttgggaaaaaaaaatgatacaatggcgatgtgcctgaatttggagtgctgacatggtaatatgcg-ctcttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACTGTTGGCTTGGTCTGTGAAAATTACAGCGGTCTGTTCAGACGACCCCGTG
|||||| ||     | |  | | |   | | ||      | | ||    |   | |||    |  ||||     ||||   |||  | | || || || | | ||||| ||||||||||||||||||||||| || ||||||||||||||||| |||||||| |||||||| || |||||||| ||  ||||||| || |||||||
gtgagcgcgctctct-cgatgttgcagtggcgatggttgattcatgagctcaaggtgtttgcgtgtttgattgtctgatgcggtggtgttcgtctgtttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACTGTTGGGTTGGTCTGCGAGAATTACAGTGGCTTGTTCAGGCGCCCCCGTG

upper sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 3
gtgagcccgtaggttgcagtatcgtgtttgggaaaaaaaaatgatacaatggcgatgtgcctgaatttggagtgctgacatggtaatatgcgctcttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACTGTTGGCTTGGTCTGTGAAAATTACAGCGGTCTGTTCAGACGACCCCGTG
        |||||||      | |||  |   |      |||  ||        | |    | ||| |       | |     |  |||  | | |  |   ||||| || ||||| || ||||| || ||||| |||||||||||||||||||| ||||| ||||| ||| |||| |||   ||  |||| ||||| || ||||
--------gtaggtttggtggtggtgcatactagctggtaatcttagcccatttaagcattttaatctaa-----taaagcaatcctat-tgatttcttatccagGTTCTTATTGATAACATCAAAGACTTTGCACCGATAATATACACTCCCACAGTTGGATTGGTGTGTCAAAACTACTCGGGGTTGTTTAGACGTCCACGTG
















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|76919658|gb|DV167819.1|DV167819
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAA
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAA
EST: gi|211274711|gb|FL015918.1|FL015918
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211274712|gb|FL015919.1|FL015919
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATA
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATA
EST: gi|71437509|gb|DR818559.1|DR818559
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211016654|gb|FL375789.1|FL375789
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|29130557|gb|CB381261.1|CB381261
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|29130494|gb|CB381198.1|CB381198
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|149102281|gb|EE287658.2|EE287658
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211384290|gb|FL369291.1|FL369291
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211048980|gb|FL422995.1|FL422995
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211527375|gb|FL402913.1|FL402913
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|32801635|gb|CD953871.1|CD953871
EST:     GATCCCCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT

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), 48 (downstream exon)
Score: 243

GGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACTGTTGGCTTGGTCTGTGAAAATTACAGCGGTCTGTTCAGACGACCCCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

GGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACTGTTGGCTTGGTCTGTGAAAATTACAGCGGTCTGTTCAGACGACCCCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

GGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACTGTTGGCTTGGTCTGTGAAAATTACAGCGGTCTGTTCAGACGACCCCGTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 129

GGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACTGTTGGCTTGGTCTGTGAAAATTACAGCGGTCTGTTCAGACGACCCCGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgatgtgcctgaatttggagtgctgacatggtaatatgcgctcttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACTGTTGGCTTGGTCTGTGAAAATTACAGCGGTCTGTTCAGACGACCCCGTG
                      tgctgac  putative branch site (score: 129)
                                        cgctcttctc  putative PPT
                                 taatat  TA-rich tract