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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattttactgcttccctgattaacttggtcgtgatatttgttagggagttcaaacatccctggtaacattattgtcttgtagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGA

Basic information

species Glycine max
transcript GLYMA17G33050.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 6
------gtatgcattttactgcttccctgattaac-ttggtcgtgatatttgttag-ggagt---tca--aacatccctggta----acattattgtcttgtagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGA
       | || |||    |||||      | | | ||   | | || |||  |||  ||||   |||    ||  | | | |    |   |||  ||||  ||| ||||||||||| |||||||||||||| |  || || ||||| |||||||| ||||| || |||||||| ||||| |||||||||||||| ||||| | 
gtatgtatgtgaattaatgtgcttaatctttgagcattcaacttcatttttcatagcagagtgtctcattggcaaactttgaactccaatctatattcttacagGCAATCACAAGAACATTTTCAATGATGCAAAGGTACCTTGGTCAGAGTACCGTTATTACGACCCCAAGACTGTTGGCTTGGATTTTGAGGGAATGATAGC

upper sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------gtatgcattttactgctt--ccctgattaacttggtcgtgatatttgttagggagttcaaacatccctggtaacatt-attgt-cttgt----agGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGA
                                                    |||  |  || |  |   | || |||   || |  |  || |    |    |  |     |   ||  |  |||| ||| | |||||    |||||| ||||||||||| |||||||||||||| || || ||||| |||||||| |||||||| |||||||| |||||||||||||||||||| ||||| | 
gtaagtatgttgatgcaactattcttcatgacttgatgtacctaccaaaatcatgactcatagtcttgggctctcattgtttttggtgaaatttgaagtgtcaaagtggcggacttctaatttcattcattctacttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC

upper sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 6
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 7
gtatgcattttactgcttccctgattaacttggtcgtgatatttgttagggagttcaaacatccctggtaacattat----tgtcttgt-agGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGA
        |  | ||  |     |  ||| |  | | |  ||||| |      || || |  |  |   |||  ||     |  |   | |||||||||||||||||| ||||||||||| |  || || ||||| || ||||| || |||||||| || ||| |||| |||||||||||||| ||||| | 
-------gtacattgtcttgaccacaaacatttttgagtgatttggtttcatatttaaccgcctttatcaactgtacaaaataccacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC

upper sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 8
gtatgcattttactgcttccctgattaacttggtcgtgatatttgt-tagggagttcaaacatccc-tggtaacattattgtctt-gtagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGA
                 |   |  |   |||| | | || |||||| |   |||| |  |  || | ||||   |  ||  |||| | ||||||||||||||||||||||||||||||||| || || |||||||| |||||||| ||||| || || |||||||| ||||||||||| || |||||   
----------------gtgagtattccccttgtttgggagatttgtgtcaagagtactgatttctcatggttgaagaatcatctttgcagGTAATCACAAGAATATTTTCAATGATGCTAGAGTTCCCTGGTCTGAATACCGATACTATGACCCAAAAACAGTTGGCTTGGATTTTGATGGGATGATATC

upper sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 6
lower sequence: PP1S245_98V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------gtatgcattttactgcttccctgattaacttggtcgtgatatttgt-tagggagttcaaacatccctggtaacattattgtcttgtagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGA
                                    ||||   ||| |  | | | |  | | || | |  | || |  || ||      |   |   |  |||   |||||   | |   |||||||||||| || || |||||||||||  |||| ||||||   |||||||| || |  ||||| ||||| || ||||||||||| || |||||||||||
gtatggatcaaactccagtcgcatacaattcacccttatgttctttccaacgtgcttcttgatctagattctaatctaagtgtatttgtcttctatggctgtggcg-cattaacattt--cagGTAATCACAAAAACATCTTCAATGATGCCGGTGTTCCATGGAAAGAGTACCGCTACTTCGATCCTAAGACCGTAGGGTTGGATTTCGAAGGCATGATTGA

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|192332683|gb|FK025340.1|FK025340
EST:     AGAGCGATATTTTCCTGGGGCAAAAGTTTTGATATCAGCTCCTACCTGGG                         GTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACC
genomic: AGAGCGATATTTTCCTGGGGCAAAAGTTTTGATATCAGCTCCTACCTGGGgtatgcattt ... tgtcttgtagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACC
EST: gi|120532068|gb|EH260201.1|EH260201
EST:     AGAGCGATATTTTCCTGGGGCAAAAGTTTTGATATCAGCTCCTACCTGGG                         GTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACC
genomic: AGAGCGATATTTTCCTGGGGCAAAAGTTTTGATATCAGCTCCTACCTGGGgtatgcattt ... tgtcttgtagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACC
EST: gi|120532359|gb|EH260492.1|EH260492
EST:     AGAGCGATATTTTCCTGGGGCAAAAGTTTTGATATCAGCTCCTACCTGGG                         GTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACC
genomic: AGAGCGATATTTTCCTGGGGCAAAAGTTTTGATATCAGCTCCTACCTGGGgtatgcattt ... tgtcttgtagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgtgatatttgttagggagttcaaacatccctggtaacattattgtcttgtagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGA
                                 tggtaac  putative branch site (score: 2)
                                            ttgtctt  putative PPT
      atatttgtta  TA-rich tract