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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttaatttgtgatggaatcatttccccaatttacaaataatttgggggttaagacaacagtgaatttaaatggttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT

Basic information

species Glycine max
transcript GLYMA17G13440.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
gtaagtatttaatttg-tgatgg-aatcat---ttccccaatttacaaataatttgggggttaagacaacagtgaatttaaatggtt--ttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT
|||||||  | ||| | | |||| ||| ||    |  ||||   | | |       |  | | | |||   |||||||| ||||| |  |   ||||| | |||||| ||||||||||||||||| |||||||| |||||||||| ||| |||||||| || ||||  || || || ||| ||| || |||||| |
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT

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

upper sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G179308_T01 (Zea mays), 3'ss of exon 5
gtaagtat----ttaatttgtgatgg--aatcatttccccaatttacaaataatttgggggttaagacaacagtgaatttaaatggtt--ttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT
|||||||     |||  |||||      |   | |  |||||      ||  || ||| | |||| |||   ||||||||  ||   |  | | ||||| |||||||  ||||||||||||||||| |||||||| ||| |||||| ||| |||||||| || ||||  || || || ||||||| || |||||| |
gtaagtacattgttagattgtggcaattatgaactgacccaaaaagataaccatgtggtgcttaa-acattggtgaatttggatcaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGCGGGAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGATTGCCAAACAACTGT

upper sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtatttaat-----ttgtgatgga-atcattt-ccccaatttacaaataatttgggggttaagacaacag-tgaatttaaa-tggttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT
||||||||||| |     ||||||||   || |||| ||||  |||   ||  | |||||| | ||       | |||| ||||| |||||   |||||| |||||||| |||||| | || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| | ||||| |
gtaagtatttagtcaattttgtgatgtctatgattttccccggtttgggaaatagttggggttgaattttgtggatgaacttaaaatggttgctacagGTATTTGAGAAGCTTGGATCGAGTTTATACGATTTTCTTCGGAAAAACAATTATCGCTCCTTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTCT

upper sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtat----ttaatttgtgatggaatcatttccccaattt-acaaataatttgggggttaagacaaca---gtgaatttaaatggttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT
||||||||    || | || ||||||  | ||||||||||||| || |||| |||||||||||||||        |||||| ||||||||| |||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |
gtaagtataaaattgaattatgatggcttgatttccccaatttcacgaatattttgggggttaagactttgtggatgaattcaaatggtttcaacagGTGTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTACGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTGT

upper sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------gtaagtatttaatttgtgatggaatcatt--tccccaatttacaaataatttgggggttaagacaacagtgaatttaaatggttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT
               | || | |||||  ||    |  | ||  ||      || ||  ||   |   ||| | ||      | ||  |   |  | ||  ||||| | ||| | ||| ||||| |||||||||||||| ||||| ||||||||||||||  ||||| |    ||||| || || ||  ||||| | || || |
ttctagatacagttcaggtgtataatt-atgtccaatcccttgttcttggccttgcatttatagtaatggtcatgat--tgttcaaactgggtaatcttg-cagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT

upper sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S425_6V6.2 (Physcomitrella patens), 3'ss of exon 5
---gtaagtatttaatttgtgatggaatcatttccccaatttacaaataatttgggggttaagaca-acagtgaattta------aatggt--tttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT
     | | |||       ||| |   |    | |    |||  || || |    |  ||||| |    | |   |||       | ||||  ||   |||||||  ||||  || || ||||| || |||||||||||||| ||||||||||||||  | ||| |    |||||||| || ||  ||||| | ||||| |
tatccagggattcgcacattga-gttcttggatacaacgtttgaaattactccctgaattaaggcgcgtacttcttttgtttactattggtaattatgcagGTGTGCGAGAGGCTGGGGCCAAGTTTGTACGATTTTCTTCGAAAAAACAATTATCGACCGTTTTCTGCAGATCTTGTTCGAGATTTTGGCCGCCAACTCT

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|207776596|gb|GD747468.1|GD747468
EST:     TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT                         GTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAAT
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATTgtaagtattt ... gttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAAT
EST: gi|192295348|gb|FG986002.1|FG986002
EST:     TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT                         GTGCTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGG
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATTgtaagtattt ... gttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGG
EST: gi|17518814|gb|BM187856.1|BM187856
EST:     TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT                         GTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAAT
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATTgtaagtattt ... gttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAAT
EST: gi|9986568|gb|BE660676.1|BE660676
EST:     TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT                         GTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAAT
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATTgtaagtattt ... gttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAAT
EST: gi|9901661|gb|BE610629.1|BE610629
EST:     TTGTGTGCAAATACGGGACTCGTTTGACTATCGTCATCATATCTGTATT                         GTGTTTGAGAA
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATTgtaagtattt ... gttttaacagGTGTTTGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttacaaataatttgggggttaagacaacagtgaatttaaatggttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT
                                   aatttaaatggtttta  TA-rich tract