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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttgattgatttgtgatggattgatttccccaatatacataatgggggttaagggtgaattcaaatggttgcaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT

Basic information

species Glycine max
transcript GLYMA04G36360.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
gtaagtatttgattgatttgtgatggat-tgatttccccaatatacataa-----tgggggttaag----ggtgaattcaaatggttgc--aacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT
|||||||  | |||   || ||     | |||  |  |||| | | ||||     ||  | ||||     ||||||||  ||||| ||     ||||| | |||||| ||||||||||||||||| |||||||| |||||||||||||| || ||||| || ||||  || || || ||| ||| |   |||||||
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT

upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G179308_T01 (Zea mays), 3'ss of exon 5
gtaagtatttgattgatttgtgatggat-tgatttccccaatatacataa-----tgggggttaag----ggtgaattcaaatggttgc--aacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT
|||||||  |  ||   |||||     | |||  |  || | | | ||||     ||| | ||||     ||||||||   ||   ||   | ||||| |||||||  ||||||||||||||||| |||||||| ||| |||||||||| || ||||| || ||||  || || || ||||||| |   |||||||
gtaagtacattgttagattgtggcaattatgaactgacccaaaaagataaccatgtggtgcttaaacattggtgaatttggatcaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGCGGGAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGATTGCCAAACAACTGT

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

upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtatttgattgattt-gtgatgg--attgatttccccaatat---acataatgggggttaa-------gggtgaattcaaa-tggttgcaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT
||||||||||  |  |||| ||||||   ||   |||||||  | |   | ||| | |||||| |       || |||| | ||| ||||||| |||||| |||||||| |||||| | || ||||||||||||||||||||||||| |||||| || |||||||||||||||||||||||||||||||||||||| |
gtaagtatttagtcaattttgtgatgtctatgattttccccggtttgggaaatagttggggttgaattttgtggatgaacttaaaatggttgctacagGTATTTGAGAAGCTTGGATCGAGTTTATACGATTTTCTTCGGAAAAACAATTATCGCTCCTTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTCT

upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtatttgattgatttgtgatggattgatttccccaatat-----acataatgggggttaag--------ggtgaattcaaatggttgcaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT
||||||||   ||||| || |||||| |||||||||||||| |     | ||  |||||||||||        | ||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||| |||||| ||||||||||||||||||||||||||||||||| | |||||||
gtaagtataaaattgaattatgatggcttgatttccccaatttcacgaatattttgggggttaagactttgtggatgaattcaaatggtttcaacagGTGTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTACGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTGT

upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------gtaagtatttgattgatttgtgatggattgatttc--cccaatatacataatgggggttaagggtgaattcaaa-tggttg---caacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT
               | || | | ||| || |   ||   ||| | |   ||    ||  ||| |   ||| | |  ||  |||||| ||| |       ||||| | ||| | ||| ||||| |||||||||||||| ||||| ||||||| ||||||  ||||| |    ||||| || || ||  ||||| | || ||||
ttctagatacagttcaggtgtataatt-atgtccaatcccttgttcttggccttgcatttatagtaatggtcatgattg--ttcaaactgggtaatcttgcagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT

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|15285557|gb|BI469448.1|BI469448
EST:     TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT                         GTGTTTGAGAAACTT
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATTgtaagtattt ... gttgcaacagGTGTTTGAGAAACTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttccccaatatacataatgggggttaagggtgaattcaaatggttgcaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT
 gattgat  putative branch site (score: 4)
         aatatacataat  TA-rich tract