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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatacctagggctgacaatgggctgtaaattttacactataagatttaaggatcgagtcgggttaggatcgggctttatttcaagtcatttttgaactataatttatttagggccttgacattttgtgaagaaccatttggatcacaatccattaccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG

Basic information

species Zea mays
transcript GRMZM2G161969_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 17
gtgatacctagggctgacaatgggctgtaaattttacactataagatttaaggatcgagtcgggttaggatcgggc-tttatttcaagtcatttttgaactataatttatttagggccttgacattttgtgaagaaccatttggatcacaatccattaccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG
                                                     ||  | |   | || ||  |  | || |  |       || |||    || ||| |  |||||  |    ||||  | ||   || |||   |       ||            |||||||||||   ||  || || | ||||||||||||||| |||||||| || ||| |||||||||| ||||||||||| ||||
-----------------------------------------------------ataaacttctgctaagaaggtccattcacgttgcagtgttcttgtg--atgatt-acatagggtgtcattatttacttaatggccttttttttgtttggacagCTGAGAAGAGGGTGATACCTGGCAGCGTAGACGGCCAGTATGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG

upper sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 17
gtgatacctagggctgacaatgggctgtaaattttacactataagatttaaggatcgagtcgggttaggatcgggctttatttcaagtcatttttgaactataatttatttagggccttgacattttgtgaagaaccatttggatcacaatccattaccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG
                                                 | | ||    |  | |  | |      || | ||  ||||||  | |   ||     ||  |||||  |     ||   | ||   |  ||| | |       ||            |||||||||||   |||| ||||||  || ||||||||||| |||||||| || ||| |||||||||| ||||||||||| ||||
-------------------------------------------------atgtattctatttgctaggcaggctcattcactt--agtcatgct-gttttagtccgtacatagggattcatttttaactcaactgcttttttgcttggg---cagCTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG
















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|20301579|gb|BQ164522.1|BQ164522
EST:     GGCTATTGGTTCTGCCGAGAAGAGGG                         TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
genomic: GGCTATTGGTTCTGCCGAGAAGA-GGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
EST: gi|20336914|gb|BQ172544.1|BQ172544
EST:     TGGTTCTGCCGAGAAGAGGG                         TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
genomic: TGGTTCTGCCGAGAAGA-GGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
EST: gi|71329666|gb|DR801555.1|DR801555
EST:     GGCTATTGGTTCTGCCGAGAAGAGGG                         TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
genomic: GGCTATTGGTTCTGCCGAGAAGA-GGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
EST: gi|113659135|gb|DW816431.1|DW816431
EST:     GGCTATTGGTTCTGCCGAGAAGAGG                         G
genomic: GGCTATTGGTTCTGCCGAGAAGAGGgtgataccta ... ccacccttag-
EST: gi|113659135|gb|DW816431.1|DW816431
EST:     GGCTATTGGTTCTGCCGAGAAGAGG                         G
genomic: GGCTATTGGTTCTGCCGAGAAGAGGgtgataccta ... ccacccttag-
EST: gi|21809699|gb|BQ668017.1|BQ668017
EST:     GGCTATTGGTTCTGCCGAGAAGAGGG                         TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
genomic: GGCTATTGGTTCTGCCGAGAAGA-GGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
EST: gi|5439400|gb|AI820321.1|AI820321
EST:     GGCTATTGGTTCTGCCGAGAAGAGGG                         TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
genomic: GGCTATTGGTTCTGCCGAGAAGA-GGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
EST: gi|20208397|gb|BQ134486.1|BQ134486
EST:     GGCTATTGGTTCTGCCGAGAAGAGGG                         TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
genomic: GGCTATTGGTTCTGCCGAGAAGA-GGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
EST: gi|5343148|gb|AI795333.1|AI795333
EST:     GGCTATTGGTTCTGCCGAGAAGAGG                         G
genomic: GGCTATTGGTTCTGCCGAGAAGAGGgtgataccta ... ccacccttag-
EST: gi|5343148|gb|AI795333.1|AI795333
EST:     GGCTATTGGTTCTGCCGAGAAGAGG                         G
genomic: GGCTATTGGTTCTGCCGAGAAGAGGgtgataccta ... ccacccttag-
EST: gi|148935652|gb|EC879696.2|EC879696
EST:     GGCTATTGGTTCTGCCGAGAAGAGGG                         TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
genomic: GGCTATTGGTTCTGCCGAGAAGA-GGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
EST: gi|4776441|gb|AI665444.1|AI665444
EST:     GGCTATTGGTTCTGCCGAGAAGAGGG                         TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA
genomic: GGCTATTGGTTCTGCCGAGAAGA-GGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCA

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: 171

CCGAGAAGAGGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 267

CCGAGAAGAGGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 165

CCGAGAAGAGGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 315

CCGAGAAGAGGgtgataccta ... ccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggccttgacattttgtgaagaaccatttggatcacaatccattaccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG
   ccttgac  putative branch site (score: 315)
                                             ccaccctt  putative PPT
        acatttt  TA-rich tract