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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttaggtggaaaagattaatcttcatgtccataaattacctatgtagctactaatgccatttttctactctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG

Basic information

species Glycine max
transcript GLYMA17G10640.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 4
------------gtaagt-tttaggtg-----gaaaagattaatcttcatgtccataaattacctatgtagctactaatgccatttttctactctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
            | |||   ||| ||      ||| ||  | || ||  |||   |  |||   | |     | ||||     |  || ||   ||   ||||||||| ||||| || || || || |||||| |||||||||||||||| || |||||||||||||||||||||||||| || ||||||
tgctacttgtgtggaagcacttatgtaccttagaatagcatgatattgttgtatctccatttgttttact-ttcctaacattttccttttatcatgtacagTTTATGCTGATGGGAGCATATGCTTAGATATACTACAAAACCAGTGGAGCCCCATATATGATGTAGCTGCTATACTCACATCCATCCAG

upper sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
gtaagttttaggtggaaaagattaatcttcatgtccataaattacctatgtagctactaatgccatttttctactctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
     | |||  |  |  |   || | |     || |      || ||| |   |     || |||||||||  | ||   ||||||||| |||||||| || || || |||||  | || || ||||||||||| ||||||||||||||||| |||||||| || ||||||
-----tcttaactatatgatggtactatct---tctaatgcccacttatatgtgtcaccctgacatttttctcatatgc--agtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

upper sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 2
--------------------gtaagttttaggtggaaaagattaatcttcatgtccataaattacctatgtagctactaatgccatttttctactctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
                      || | |       | | |||    ||   | || |      || ||| |   |     || |||||||||  | ||   ||||||||| |||||||| || || || |||||  | || || ||||||||||| ||||||||||||||||| |||||||| || ||||||
ctcctctggcttattctgatacaactctcttaactatatgatggtactatct-tctaatgcccacttatatgtgtcaccctgacatttttctcatatgc--agTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

upper sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtt----ttaggtggaaaagattaat-cttcatgtccataaattaccta--tgtagctactaatgccatttttctactctggga-----agTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
|||||||     || || | ||  | ||   ||||||||  |  | ||   ||  ||  | | || |   |    || || | ||        ||| ||||| ||||||||||||||| | |||||  ||||||| |||||||||||||||||||||||||| |||||||| || ||||| |||
gtaagttggaactatgttgcaattagtatcacttcatgttaaatatttctttagctgcggtttcttacttctaccttttattttgaattggccagTCTATGCAGATGGAAGTATTTGTCTCGATATTCTACAAAATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG

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|6846800|gb|AW349090.1|AW349090
EST:     AAACAAGCCACCAACTGTACGATTTGTNNNNCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|254335070|gb|GR844855.1|GR844855
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|16106211|gb|BI893951.1|BI893951
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|254335069|gb|GR844854.1|GR844854
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|15001308|gb|BI322122.1|BI322122
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|10235145|gb|BE804033.1|BE804033
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|192331367|gb|FK021035.1|FK021035
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|21888252|gb|BQ741465.1|BQ741465
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|192330437|gb|FK021196.1|FK021196
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|254331190|gb|GR843309.1|GR843309
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|192330438|gb|FK021197.1|FK021197
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|16996966|gb|BM086338.1|BM086338
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|208058951|gb|GD858983.1|GD858983
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAA-CCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|254317222|gb|GR826167.1|GR826167
EST:     AAACAAGCCACCAACTGTACGA-TTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|192331366|gb|FK021034.1|FK021034
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|8284603|gb|BE022162.1|BE022162
EST:     AGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTCATGCGCATGCAAGTATCTGTTTGCATATATCACAAAACCAGTGGAGTC
genomic: AGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|14259666|gb|BG882574.1|BG882574
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|254317221|gb|GR826166.1|GR826166
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagtttta ... ctctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtccataaattacctatgtagctactaatgccatttttctactctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
                          tactaat  putative branch site (score: 1)
                                  ccatttttctactct  CT-rich tract
        ataaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttaggtggaaaagattaatcttcatgtccataaattacctatgtagctactaatgccatttttctactctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT