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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaatatacttttatttattaatatttgaagtcttatgttatacagtagatagtctttaattatttactgaaatgtttgatttgcatgtatttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGTTTTGCTGATGGTGAGATATATGTCCAGCTGCAAGAGAGTGTCAGGGGGT

Basic information

species Glycine max
transcript GLYMA07G12660.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G12660.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038791_T01 (Zea mays), 3'ss of exon 2
-ttgaatatacttttatttattaatatttgaagtcttatgttatacagtagatagtctttaattatttactgaaatgtttgatt-tgcatgtatttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGTTTTGCTGATGGTGAGATATATGTCCAGCTGCAAGAGAGTGTCAGGGGGT
  | |||| | ||||| | |  |||| ||  |  |  | |  |||   ||  | ||   |   || | | |    | |   ||  || || | | | |  |||| || ||| | ||| |||| || || || || || |  |  |||||| | |||||||||||||| |||||||| ||| ||||||| |||||  |||| |
cctcaatagatttttaatgacgaataattataaac--aggaaatatgttatctcgttcatgcctaataatttctttatggtatcctgtatttttatgaacagGAGATAGCAAGTTACTTGGGGCTAGAACTTGGGAAGATAACCATAAAGAGGTTTGCTGATGGTGAAATATATGTTCAGTTGCAAGAAAGTGTACGGGGCT

upper sequence: GLYMA07G12660.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G44530.2 (Arabidopsis thaliana), 3'ss of exon 2
ttgaatatacttttatttattaatatttgaagtcttatgttatacagtagatagtctttaattatttactgaaatgtttgat-ttgcatg-tatttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGTTTTGCTGATGGTGAGATATATGTCCAGCTGCAAGAGAGTGTCAGGGGGT
 |   |  | ||  |   ||||  ||| | |      || | || |||  ||| |||  |||  | |  |    |  ||| | ||  | | |  | |   |||| ||| | |||||  |||| ||||| || || ||||  ||||| || || ||||||||||||||||| ||||| ||||| ||||||||||| ||||| |
atttgttcaattgcaaagattaggattaggaagaaattggtttagagt--atattctggaatcgtcttgtttgttcattggtgttttacgctgatgatacagGAGATTTCTTGCTATTTGGGTCTGGACCTTGGGAAAATCAAGATTAAACGCTTTGCTGATGGTGAGATCTATGTTCAGCTACAAGAGAGTGTAAGGGGAT

upper sequence: GLYMA07G12660.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 3'ss of exon 2
-----ttgaatatacttttatttattaatatttgaagtcttatgttatacagtagatagtctttaattatttactgaaatgtttgatttgcatgtatttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGTTTTGCTGATGGTGAGATATATGTCCAGCTGCAAGAGAGTGTCAGGGGGT
     |||   ||  |||| ||| ||  | ||| |   |   ||||   |    ||   | | ||  | |        |||  | |||   |||| ||   ||||||||||||||||||| ||||||||||||| |||||||  || ||||| || ||||||||||| ||||| ||||| ||| ||||||||||||| || ||||
actttttgtgcatgtttttttttttttttttttcata-caagtgtttctcccatgaccttttgtatgtgtcattcctgatgcataatt---atgt-ttgttgtagGAAATTGCATGCTACATGGGCCTGGAGCTGGGAAAAATAAACATAAAACGCTTTGCTGATGGAGAGATTTATGTTCAGTTGCAAGAGAGTGTTAGAGGGT

upper sequence: GLYMA07G12660.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S123_105V6.1 (Physcomitrella patens), 3'ss of exon 2
ttgaatatacttttatttattaatatttgaagtcttatg-ttatacagtagata-gtctttaattatttactgaaatgtttgatttgcatgtatttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGTTTTGCTGATGGTGAGATATATGTCCAGCTGCAAGAGAGTGTCAGGGGGT
 || |  |  |  | |  ||       | || | | |||  |  |  |     | |   || |  |       |   || |   |||   |   ||  | ||||||| || |  ||  ||||||| ||  | ||||| | ||  |||||||| || || |||||||| || ||||| |||||||||||||||||  | || |
atgcagttcgtcgtgtgcatgtcctggtaaaatttaatggcttcattgcgaccaagaactttaacacacgtgaattcgtcttggttgttcgccatt--gcagGAAATCGCTTATTATATGGGCCTTGATTTGGGAAAGATTACAATAAAGCGCTTCGCAGATGGTGAAATTTATGTACAGCTGCAAGAGAGTGTACGTGGTT

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|254348826|gb|GR852505.1|GR852505
EST:     ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAG                         GAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
genomic: ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAGgtcgtgcttc ... atttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
EST: gi|298185832|gb|HO030993.1|HO030993
EST:     ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAG                         GAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
genomic: ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAGgtcgtgcttc ... atttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
EST: gi|4313916|gb|AI461035.1|AI461035
EST:     ACACTCGCCTNCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAG                         GAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATANAGCGT
genomic: ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAGgtcgtgcttc ... atttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
EST: gi|27446243|gb|CA953366.1|CA953366
EST:     ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAG                         GAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
genomic: ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAGgtcgtgcttc ... atttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
EST: gi|16997052|gb|BM086424.1|BM086424
EST:     ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAG                         GAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
genomic: ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAGgtcgtgcttc ... atttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
EST: gi|209708416|gb|BW665391.1|BW665391
EST:     ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAG                         GAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT
genomic: ACACTCGCCTCCGGATATTCTCCGGCACCGCCAATCCGGCGCTCGCTCAGgtcgtgcttc ... atttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagatagtctttaattatttactgaaatgtttgatttgcatgtatttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGTTTTGCTGATGGTGAGATATATGTCCAGCTGCAAGAGAGTGTCAGGGGGT
           tttaattatttactga  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaatatacttttatttattaatatttgaagtcttatgttatacagtagatagtctttaattatttactgaaatgtttgatttgcatgtatttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGTTTTGCTGATGGTGAGATATATGTCCAGCTGCAAGAGAGTGTCAGGGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt