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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaattccaactccaattccaatttgtgggaaggagatgtaaaatcaaaatcctaccatgaacctatagcgataacaaagttttgtaatttgtatcacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTAGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG

Basic information

species Glycine max
transcript GLYMA08G22840.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G117531_T04 (Zea mays), 3'ss of exon 9
gcaattccaactccaattccaatttgtgggaaggagatgtaaaatcaaaatcctaccatgaac--ctatagcgataacaaagttttgtaatttgtatcacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTAGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG
  || | ||     ||| | |     ||  |   |   || |  |          | | | |   || |   ||||  |||   |  | || | |||  ||| ||||| ||||||||||| ||||| |||||| |||| ||||||||||| || |  ||  |||| ||| | ||  || |||  ||||| |      |  | 
-aaagttcattctgaatacaagcaattgatatatactagtcatgtgggcccttggcaacgtattgctgttctgatacaaaaaaatgatcatct-tattgcagTTGGGAAAAACCAATACTGCTTGCATGGGGAATATCTGACAAGTACTTACCGCTCTCGATAGCTGAGGAATTCAAGCAAGCTAATCCTGGCGTTGTAAAA

upper sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 9
gcaattccaactccaattccaatttgtgggaaggagatgtaaaatcaaaatcctaccatgaacctatagcga-taacaaagttttgtaatttgtatcacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTAGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG
     |  |  | |||     |  |||          |       |  |   |  |  | |   ||    || | |  ||    ||   || | |   ||| |||||||||||||||||| |||| |||||| |||||||||||||  |||| || || || |||||  ||||||| || ||||| || |   | ||  | 
-tttgtgtattttcaaaattcacctgtaaactattcttcatgctgctgacctcgccttttattttaccatgaattatgaatgaatgactttgggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCCTCAATCAGTGGCAGAAGAGTTTCAAAAGGGAAACCCTGATTATATAAAA
















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|120491597|gb|EH219764.1|EH219764
EST:     ACTTNCAA-GGTACTTTCAGTGAAATAGCAGCAGGATTTGCAACTGACAG                         ATGGGATAAACCAATACTACTTGC
genomic: ACTT-CAAAGGTACTTTCAGTGAAATAGCAGCAGGATTTGCAACTGACAGgtatatttat ... tgtatcacagATGGGATAAACCAATACTACTTGC
EST: gi|120491643|gb|EH219810.1|EH219810
EST:     AACTTCAAAGGTACTTTCAGTGAAATAGCAGCAGGATTTGCAACTGACAG                         ATGGGATAAACCAATACTACTTGCTT
genomic: AACTTCAAAGGTACTTTCAGTGAAATAGCAGCAGGATTTGCAACTGACAGgtatatttat ... tgtatcacagATGGGATAAACCAATACTACTTGCTT
EST: gi|6914784|gb|AW396314.1|AW396314
EST:     AACTTCAAAGGTACTTTCAGTGAAATAGCAGCAGGATTTGCAACTGACAG                         ATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATAGCAGCAGGATTTGCAACTGACAGgtatatttat ... tgtatcacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaatcctaccatgaacctatagcgataacaaagttttgtaatttgtatcacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTAGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG
                        cgataac  putative branch site (score: 3)
                               aaagttttgtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaattccaactccaattccaatttgtgggaaggagatgtaaaatcaaaatcctaccatgaacctatagcgataacaaagttttgtaatttgtatcacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTAGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
-caattcc
- - - ccaactc
- - - - - - - - - - - -ttgtggg