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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatatggtgcttaaacgttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT

Basic information

species Zea mays
transcript GRMZM2G063792_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
gtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatatggtgcttaaacgttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT
||||||||||  |||||||||| |||||||| ||| ||| ||| | ||||||  |||  |||||||| |||||||||||| ||  |||||| |||||||| ||||| |||||||||||||||||||||||||||| ||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT

upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G02740.3 (Glycine max), 3'ss of exon 4
gtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatatggtgcttaa-acgttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT
|||||||  |  || | | |||  |    | | |  |   | |||||     || ||| | |||| ||   |||||||||  ||   |  | | ||||| |||||||  ||||||||||||||||| ||||||||  ||||||||||||| |||||||| || ||||  || || || ||| ||| ||||||||| |
gtaagtatttaatttg-tgatggaatcatttccccaatttacaaata-----atttgggggttaagacaacggtgaatttaaatggtt--ttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAAACAACTAT

upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 4
gtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatatggtgcttaaacgttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT
|||||||  |  ||   || |||     ||  | |  |||||   ||||   | |||| | ||||     ||||||||   ||   ||   | ||||| |||||||  ||||||||||||||||| ||||||||  ||||||||| ||| || ||||| || ||||  || || || ||| ||| |   ||||| |
gtaagtatttgattgatttgtgatgg--attgatttccccaa---tatacata-atgggggttaag----ggtgaattcaaatggttgc--aacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTAT

upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 4
gtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatatggtgcttaaacgttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT
|||||||  |  ||   || |||     ||  | |  |||||   ||||   | |||| | ||||     ||||||||   ||   ||   | ||||| |||||||  ||||||||||||||||| ||||||||  ||||||||| ||| || ||||| || ||||  || || || ||| ||| |   |||||||
gtaagtatttgattgatttgtgatgg--attgatttccccaa---tatacata-atgggggttaag----ggtgaattcaaatggttgc--aacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT

upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
gtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatatggtgcttaa-acgttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT
|||||||  |  || | | |||  |    | | |  |   | |||||     || ||| | |||| ||    ||||||||  ||   |  | | ||||| |||||||  ||||||||||||||||| ||||||||  ||||||||||||| |||||||| || ||||  || || || ||| ||| || |||||| |
gtaagtatttaatttg-tgatggaatcatttccccaatttacaaata-----atttgggggttaagacaacagtgaatttaaatggtt--ttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT

upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtacattgttagatt-atgacaattatgcactgacccaaaaatataaccatatggtgcttaaac--gttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT
|||||||  | || |  ||  |||    ||||   |  |||        ||  |  ||| | | ||    || | |||| ||  | |  | |  | ||||| ||||||| ||||||| | || ||||| ||||||||  ||||||||||||| ||||| || || ||||  || || || ||| ||| |   ||||| |
gtaagtatttagtcaattttgtgatgtctatgattttccccggtttgggaaatagttggggttgaattttgtggatgaacttaaaatggttgcta-cagGTATTTGAGAAGCTTGGATCGAGTTTATACGATTTTCTTCGGAAAAACAATTATCGCTCCTTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTCT

upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatat-ggtgcttaaacgttggtgaatttggattaatggtg--agcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT
||||||| |   ||  |||||||    | || | |  |||||    |  |  || | || | ||||   || ||| ||       ||||||   | ||||| ||||||| |||||||||||||||||| ||||||||  ||||||||||||| |||||||| || ||||  || || || ||| ||| || ||||||||
gtaagtataaaattgaattatgatggct-tg-atttccccaatttcacgaatattttgggggttaagactttgtggatgaattcaaatggtttcaacagGTGTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTACGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTGT

upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatat-ggtgcttaaa---cgttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT
||||||| ||   |   ||| ||  || ||| | |  |||||    || |  || | || |||||||    ||| ||||||||  ||      | | ||||| ||||||| |||||||||||||||||| ||||||||  ||||||||||||| |||||||| ||| |||  ||||| || ||| ||| || ||||||||
gtaagtatatgactgatttacgatgat-atg-atttccccaacttcatgaatattttggggcttaaaacttgttagtgaatttaaatggtc--ttaacagGTATTTGAGATGCTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGT

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|7162469|gb|AW520091.1|AW520091
EST:     TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT                         GTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAAT
genomic: TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAAT




















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: 48 (upstream exon), 46 (downstream exon)
Score: 86

TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 70

TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 87

TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT


Block sizes: 39 (upstream exon), 45 (downstream exon)
Score: 89

TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatataaccatatggtgcttaaacgttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT
                                       gattaat  putative branch site (score: 89)
                                        attaat  TA-rich tract