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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcactgcaggcatctttagtgtgcagtatgattaccaaagttttcttgacgcttaaacggatgattacatatgagattcttttcgagacaattttttatccagaagtggttgcaacttgattttctgtagtttatatgagtttctcaccataaaacatatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT

Basic information

species Zea mays
transcript GRMZM2G044092_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044092_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 6
gtaagtcactgcaggcatctttagtgtgcagtatgattaccaaagttttcttgacgcttaaacggatgatt-acatatgagattcttttcgagacaattt-tttatccagaagtggttgcaa-cttgattttctgtagtttatatgagtttctcaccataaaacatatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT
||||| |||| | | |||||||| | |||| |||||||   |||||  | |  ||    | |      ||| | |   || ||| || |  |||  | |  ||||     ||||| |||||| ||||||||      |||||| ||||||||| ||  | ||| |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||||| ||||||||| | |||
gtaagacactac-gacatctttactttgcactatgatttaaaaagtcatttaaacagccatataaccaatttataagggatattattattaagatgagtgatttagtttaaagtgcttgcaaacttgattt-----ggtttatgtgagtttcttactgtcaaa-atatcccagGGAGTACTTTGCACTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGAGTAAAGCATTGGATAACAATCAATGAGCCTCTTCAAACTGCAGTTAAT

upper sequence: GRMZM2G044092_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G16220.1 (Glycine max), 3'ss of exon 6
gtaagtcactgcaggcatctttagtgtgcagtatgattaccaaagttttcttgacgcttaaacggatgattacatatgagattcttttcgag-acaattttttatccagaagtggttgcaactt-gattttctgtagtttatatgagtttctcaccataaaacatatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT
                                                                        | | | |  || ||| | || ||  || || |       || ||||    ||  || |||| |  || | |||   |  |    ||    ||||| |||| |||||||||||  | ||||||||  |||||||||||| |||||| || || || ||| | ||||| || || ||||| || || ||||||||| |||||
-----------------------------------------------------------------------ccttgtaaatttgtttcctagtacctttattaagatgagtgtagttgatttttcaatattctattattga-atggtgtggttctgatgtggcatatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT
















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|76282021|gb|DV021589.1|DV021589
EST:     CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGT                         GGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTTGCAA-TTTTGGAGACA
genomic: CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTT-GCAAATTTTGGAGACA
EST: gi|148983451|gb|EE029465.2|EE029465
EST:     CAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGANCA-GATTGT                         GGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACA
genomic: CAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGA-CAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACA
EST: gi|148945621|gb|EC890879.2|EC890879
EST:     CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGT                         GGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAG
genomic: CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAG
EST: gi|149042713|gb|EE047228.2|EE047228
EST:     CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACA-GATTGT                         GGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAA-TTTTGGAGACAG
genomic: CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAG
EST: gi|71312821|gb|DR792939.1|DR792939
EST:     CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGT                         GGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAG
genomic: CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAG
EST: gi|71772492|gb|DR970424.1|DR970424
EST:     CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGT                         GGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAG
genomic: CCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAG

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), 40 (downstream exon)
Score: 59

GTATTGAGCCTTACGCAACTCTATATCATTGGGATCTTCCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 65

GTATTGAGCCTTACGCAACTCTATATCATTGGGATCTTCCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 61

GTATTGAGCCTTACGCAACTCTATATCATTGGGATCTTCCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90

GTATTGAGCCTTACGCAACTCTATATCATTGGGATCTTCCAAACAATCTTCAGAAGACTCTGGGGGGCTGGATTTCTGACAAGATTGTgtaagtcact ... catatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaacttgattttctgtagtttatatgagtttctcaccataaaacatatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT
                               ttctcac  putative branch site (score: 90)
                                       ataaaacatat  TA-rich tract