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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttcaagttttaaacatttgtgagtgtttaattagtttctctctgtttcctaatttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT

Basic information

species Glycine max
transcript GLYMA06G13140.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
gtatatttcaagttttaaacatttgtgagtgtttaattagtttctctctgtttcctaatttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT
         ||  ||   |||| | | |  ||  |            || ||   ||| || |      | || || ||| |||||||||| || || ||||| |||||| |||| |||||||||||||| ||  | ||||| ||||||||||| ||||| |||
-------gtaaccttatcacatatttaacagtccatcacacagaggact-ttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT

upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
---gta-tatttcaagttttaaacatttgtgagtgtttaattagt-ttctctctgtttcctaatttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT
    |  || |  |   | | | |   |       | || | ||   | | ||||  || |  ||           |||||||   |||||||||| || || |||||||||||| |||| || ||||||||||| ||  | ||||| ||||||||||||||||| |||
gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT

upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 10
gtatatttcaagttttaaacatttgtgagtg------tttaattagt-ttctctctgtttcctaatttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT
||||  |   ||| |   |||||    | |       | || | ||   | |  |||  || |  ||           ||||||||  |||||||||| || || |||||||||||| || | || ||||||||||| ||  | ||||| ||||||||||||||||| |||
gtatgct---agtctatcacattatcaaatagagcaatatattcagaactttacctgactcttgcttccaattgatcttttatcttacagGGAATAATTGTGATGGCTGCAACAAACTTGGCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT

upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
------gtatatttcaagttttaaacatttgtgagtgttta-attagtttctctctgtttcctaat---ttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT
      ||  |||   |||  |  |   |||||| |  ||    ||||||       | |  || |   ||  |    || ||  |  || ||||||||||||| || |||||||||||| |||||||||| |||||||| ||| | ||||| || ||||||||||||||||||
gtacttgttgattaggagtagtgtat-cttgtgattacttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT

upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 10
gtatatttcaagttttaaacatttgtgagtgtttaattagtttctctctg---tttcctaatttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT
         ||  | |  |||    || ||  ||| | | | | | ||||   |||  ||| ||    || || |||  ||||||||| |||||| | || || ||||||||| ||||||||||||||||||| ||||||||||| |||||||||||||| || |||
-------gtaacatatggacaaacttgtgttattagtgaatatttttctgcatttttttaacttggataatattttt--cttgtagGGCATAATATTGATGGCAGCAACAAACTTGCCTGATATTCTTGATCCAGCTTTAACAAGACCTGGTAGATTTGACAGGCAT

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|22523190|gb|BU082001.1|BU082001
EST:     AGACATTGCACCAACTACTTGTTGAAATGGATGGATTTGAGCAGAATGAA                         GGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCT
genomic: AGACATTGCACCAACTACTTGTTGAAATGGATGGATTTGAGCAGAATGAAgtatatttca ... tatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCT
EST: gi|22523127|gb|BU081938.1|BU081938
EST:     AGACATTGCACCAACTACTTGTTGAAATGGATGGATTTGAGCAGAATGAA                         GGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCT
genomic: AGACATTGCACCAACTACTTGTTGAAATGGATGGATTTGAGCAGAATGAAgtatatttca ... tatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCT
EST: gi|19348886|gb|BM893418.1|BM893418
EST:     AGACATTGCACCAACTACTTGTTGAAATGGATGGATTTGAGCAGAATGAA                         GGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCT
genomic: AGACATTGCACCAACTACTTGTTGAAATGGATGGATTTGAGCAGAATGAAgtatatttca ... tatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttaattagtttctctctgtttcctaatttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT
                        tcctaat  putative branch site (score: 2)
                                         tctttatctt  putative PPT
                           taatttattcaacatc  TA-rich tract