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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtaaattattaagacaccacccatttcaactaaattcatttatttattatatatctacctgaaacttctattttcaatttttttaactttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGAGGCTACATGGAAATCCTGGAAAATCATCCCCAGCTCTTGCTGTCAAGAA

Basic information

species Glycine max
transcript GLYMA13G25740.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G25740.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0067g01260.t01 (Vitis vinifera), 3'ss of exon 1
ctgtaaattattaagacaccacccatttca--actaaattcatttatttattatatatctacctga-aacttctattttcaatttttttaactttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGAGGCTACATGGAAATCCTGGAAAATCATCCCCAGCTCTTGCTGTCAAGAA
   | ||||||||| | |  |    ||| |  | |  |     ||||   || ||  |     | | ||||  ||| ||  || ||  |    | ||  | ||   |||| |||  ||| ||||||   || || || || ||  | ||||||||| |||||||||||||||| ||| |||| |||   ||||||||||| ||
--atgaattattaacaaagaagttgtttaattatttcagcagcttataccttgtaatttcttttaacaactcttatctttgatgttcatt-tgtaataaatagCTGGAGAAAGGGCCCAACGTGAACGCCTTCGGGACTTAGCTGTGTTTGAGAGGTTACATGGAAATCCTGGGAAAACATCTCCAAGCCTTGCTGTCAAAAA

upper sequence: GLYMA13G25740.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0067g01430.t01 (Vitis vinifera), 3'ss of exon 1
ctgtaaattattaagacaccacccatttca--actaaattcatttatttattatatatctacctga-aacttctattttcaatttttttaactttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGAGGCTACATGGAAATCCTGGAAAATCATCCCCAGCTCTTGCTGTCAAGAA
   | ||||||||| | |  |    ||| |  | |  |     ||||   || ||  |     | | ||||  ||| |   || ||  |    | ||  | ||   |||| |||  ||| ||||||   || || || || ||  | ||||||||| |||||||||||||||| ||| |||| |||   ||||||||||| ||
--atgaattattaataaagaagttgtttaattatttcagcagcttatactttgtaatttcttttaacaactcttatctctgatgttcatt-tgtaataaatagCTGGAGAAAGGGCCCAACGTGAACGCCTTCGGGACTTAGCTGTGTTTGAGAGGTTACATGGAAATCCTGGGAAAACATCTCCAAGCCTTGCTGTCAAAAA
















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|193724245|gb|FK662293.1|FK662293
EST:     ATTTTGTTGGAACATGTCCTTACATGTGCCCAG                         AAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
genomic: ATTTTGTTGGAACATGTCCTTACATGTGCCCAGgtaaacactt ... ttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
EST: gi|213604413|gb|DB970617.1|DB970617
EST:     TGCACAGCCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAG                         AAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
genomic: CGCACAACCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAGgtaaacactt ... ttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
EST: gi|254324919|gb|GR834344.1|GR834344
EST:     CGCACAACCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAG                         AAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
genomic: CGCACAACCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAGgtaaacactt ... ttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
EST: gi|298189495|gb|HO037898.1|HO037898
EST:     CGCACGACCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAG                         AAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
genomic: CGCACAACCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAGgtaaacactt ... ttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
EST: gi|298177932|gb|HO023781.1|HO023781
EST:     CGCACAACCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAG                         AAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
genomic: CGCACAACCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAGgtaaacactt ... ttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
EST: gi|193535726|gb|FK493530.1|FK493530
EST:     TGCACAGCCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAG                         AAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA
genomic: CGCACAACCATCTTCCAATTTTGTTGGAACATGTCCTTACATGTGCCCAGgtaaacactt ... ttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattatatatctacctgaaacttctattttcaatttttttaactttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGAGGCTACATGGAAATCCTGGAAAATCATCCCCAGCTCTTGCTGTCAAGAA
                                     ttttaac  putative branch site (score: 2)
                                           ctttatcc  CT-rich tract
                  aaacttctattttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtaaattattaagacaccacccatttcaactaaattcatttatttattatatatctacctgaaacttctattttcaatttttttaactttatccacagAAAGAGAGAGGATCCAGCGTGAAAAACTGCGAGATTTGGCAATTTTTGAGAGGCTACATGGAAATCCTGGAAAATCATCCCCAGCTCTTGCTGTCAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - -cacccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctgaa