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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttcagtcactggttaatgctgcccgaaatgcttgtggagcagaaatcttaacatttatgacttgtgattgttgtttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

Basic information

species Glycine max
transcript GLYMA07G01440.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 3
gtaattttcagtcactggttaatgctgcccgaaatgcttgtggagcagaaatcttaacatttatgacttgtgattgttgtttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
|||  ||  |  ||    | | ||||    ||| | | |||            |||||   | || ||||| || |   ||  ||||||| ||||| |||||  ||||||| |||||||| |||||||| || || |||||||||||||| ||||| || ||||| ||||| |||||||||||||
gtatattgta--caagactaactgcttagtgaagtacctgtaatttctgttgtttaactaatttgtcttgtcat-gcgatt--agTTTGATTATCTGAAGAGCTTGGAAATTGAAGAGAAGATTAACAAGATAAAGTGGTGCCAAACAGCAAATGGAGCATTGTTTCTTCTGTCCACAAATGATA

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 3
------------gtaattttcagtcactggttaat--gctgcccgaaatgcttgtggagcagaaatcttaacatttatgacttgtg-attgttgtttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
              ||     |  |||||  |  |    ||     ||   |  ||||         ||    ||| ||| || |   |  |   |  |||| ||||| || || ||| |||||||||| ||||| |||||||| ||||| |||||||||||||| ||    ||  | || ||  |||| ||||||||||
aggattatcttaccaagccatatgcactgcatgttagattgttattaactatcctggaatttctcaatttgtttttctgatttatatgtaatccatgtagTTCGACTACCTAAAAAGTTTGGAAATAGAGGAGAAGATTAACAAGATCAAGTGGTGCCAAACAGCCAACAACGCCCTCTTTCTCTTATCTACAAATGATA

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
--gtaatttt-cagtcactggttaatgctgcccgaaatgcttgtggagcagaaatcttaacattt-atgacttgtgattgttgt---ttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
   || | |  ||  || || | | || |        |  ||||       |   ||| | |||| || |  ||   ||||| |    ||||||||| |||||||||||  ||||||| |||||||| |||||| |||| |||||||| ||| |||| |||||||| ||||  ||||||||||||||||| |
gtatattctcacaaacattgttaagtggtat------tatttgtcttctgaattacttgaaatttgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 3
---------gtaattttcagtcactggttaatgctgcc-cgaaatgcttgtggagcagaaatcttaa-----catttatgacttgtgattgttgttt-cagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
           || |  || || |  || || ||||     | || || |   |   |||||  | |       ||| |||||| ||     ||  |  |||||||||| || || ||| |||||||||||||||| |||||||| ||||| |||||||||||| | ||   |||  | || ||  | || |||||||| |
atacatagtccaaatgacactcccaagtgaa-gctgtagttatatactggaatatgtgaaattgtgaatatttttttctgacttctgtgcaatgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 3
--gtaatttt-cagtcactggttaatgctgcccgaaatgcttgtgga--gcagaaatcttaacatttatgacttgtgattgttgtttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
   || | |  ||  || || ||| || |        | ||| || |   |   ||  || |||   | |   ||| ||| |||  | ||||||| || || |||||  ||||||| |||||||| |||||| |||| || ||||| ||| || | ||| |||| ||||| ||||||||||||||||| |
gtatattctcgcaagcattgtttagtggtattatttgt-cttatgaattacttgaaatttgaca---aagtgatgttattattgaat-agTTTGATTACCTCAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAGTGGTGTCAAGCAACAAATTGTGCATTGTTTCTTCTATCCACAAATGACA

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 3
gta-attttcagtcactggttaatgctgcccg-aaatgcttgtggagcagaaat--cttaacatttatgacttgtgattgttgtttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
||| |||   | | |       ||    |     | |  |||||   |   |    || || |    ||  ||   ||   ||||||||||||||||||| |||||| |||| ||||| |||||||| |||||||||| |||||| ||  ||||||||||||| ||||| || || || ||||| ||||
gtacattaaaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatc--tgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATA

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaattttcagtcactggttaatgctgcccgaaatgcttg--tggagcagaaatcttaacatttatgacttgtgattgttgtttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
||| ||      | ||| ||  | ||  |  |  |  |||  |  | |    ||||     || |||   | |  ||||| |  |||||||| || || |||||| |||| ||||| ||||||||||||||||| | |||||| |||||||| ||||| ||| | || || || || || |||||||
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtt-taccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
gtaattttcagtcactggttaatgctgcccgaaatgcttgtggagca--------------------gaaatcttaacatttatgacttgt-gattgttgttt-----cagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
|||  ||||  |||   |||| | ||||| ||| |   | || | ||                    ||||| ||   ||| ||| |   | | || || | |     |||||||||||||| |||||  |||||||||| |||||||| || || |||| ||||||||| ||||| ||||||||  |||| |||||||| || |||||||
gta--tttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctcactaggctctgaaatgttttaattgatgccacattgcttattctctgtgctcagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA

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|33389971|gb|CA853178.1|CA853178
EST:     GACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAG                         TTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAA
genomic: GACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAGgtaattttca ... gttgtttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAA
EST: gi|207824963|gb|GD797179.1|GD797179
EST:     GACATCCTGAGTTCCGTTATAAAGCAGAGTTTCAGAGTCATGAGCCTGAG                         TTTGACTATCTTAAGAGT
genomic: GACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAGgtaattttca ... gttgtttcagTTTGACTATCTTAAGAGT
EST: gi|208092864|gb|GD886793.1|GD886793
EST:     GACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAG                         TT-GACTATCTTAAGAGTCT
genomic: GACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAGgtaattttca ... gttgtttcagTTTGACTATCTTAAGAGTCT
EST: gi|208259705|gb|GE059735.1|GE059735
EST:     GACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAG                         TTTGACTATCTTAAGAGTCTGGAAA
genomic: GACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAGgtaattttca ... gttgtttcagTTTGACTATCTTAAGAGTCTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatgcttgtggagcagaaatcttaacatttatgacttgtgattgttgtttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
                     tcttaac  putative branch site (score: 2)
                                              ttgtttc  putative PPT
                  aaatcttaacatttat  TA-rich tract