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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaatcaaatatatcatttaaaaattgtggtggctctggattctctcctttttattatctatgagttacttaataagctcatatttatcaaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTTGTTAGGATTGATGAAGTGCTTTCCAGCCTTAAAGGAAAGCCATCGGAAG

Basic information

species Glycine max
transcript GLYMA17G04230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04230.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g22550.1 (Oryza sativa), 3'ss of exon 4
tctaatcaaatatatcatttaaaaattgtggtggctctggattctctccttt---ttattatctatgagt-tacttaataagctcatatttatca------aaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTTGTTAGGATTGATGAAGTGCTTTCCAGCCTTAAAGGAAAGCCATCGGAAG-
           |||    || |    ||| |   |||   | || ||  | |    |||     |||  |   | |  ||| || ||||||  |       ||  ||||||| ||| |  | ||| | || |||||||||||||||||||||||||| ||||||||||||||||||||  | || |||||  ||| | ||  | |   |  
----------catacaccttcatggatgtagcacctcacaaatccctaatatgagctatagcaaatgtatgcgcatcctaaacttatatttgccttttgccaatctgcagACCAAAGTTGTTCCTGCAAAGTACATCATGAAAACAGATGATGATGCTTTTGTTAGGATTGATGAAGTCATCTCAAGCCT-GAAGAAGAGTGACCCTCATG

upper sequence: GLYMA17G04230.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G160958_T01 (Zea mays), 3'ss of exon 4
----tctaa-tcaaatatatcatttaaaaattgtggtggctctggattctctcctttttattatctatgagttacttaataagctcatatttatcaaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTTGTTAGGATTGATGAAGTGCTTTCCAGCCTTAAAGGAAAGCCATCGGAAG-
    ||||| |   ||||||||    | || |    |   | |        |   ||  |  |  ||  |    |||  |    |  | | |  | |  ||||||||||||||  | ||| | || |||||||||||||| ||||| ||||| ||||||||||| ||||||||| | || ||||| |||| | ||| ||   ||  
cctttctaaattccatatatcagc--agaactagaataaatatatgcagattgtattaaaaaaattaacatagccttctt---tttgtctattgctattttgcagACAAAAATTGTTCCTGCAAAGTACATCATGAAAACGGATGACGATGCTTTTGTTAGGATCGATGAAGTGATCTCGAGCCT-AAAGAAGAGCAATTCCAATG

upper sequence: GLYMA17G04230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g00400.t01 (Vitis vinifera), 3'ss of exon 5
tctaatcaaatatatcatttaaaaattgtggtg--gctctggat-tctctcctttttattatctatgagttacttaataagctcatatttatcaaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTTGTTAGGATTGATGAAGTGCTTTCCAGCCTTAAAGGAAAGCCATCGGAAG
   |   || | | | || |||   |  | ||   | | ||  | | | |  ||       ||| | |  |   || |     |   | | | |  | ||||||| |||||| ||||| |||||||  | |||||||||||||||||||| |||||||||||||||||||| || || || |||||||||||||||||  | |
---agctaattttttaatataagcctctttgttttgttttgtttgtattttgttccccccttcttttaactctctagtgtttcctgttctttgagtaatgcagACGAAAATCCTCCCTGCTAAATATGTAATGAAAACAGATGATGATGCTTTTGTTAGGATTGATGAAGTTCTCTCAAGTCTTAAAGGAAAGCCATCTAATG

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|193344416|gb|FK311168.1|FK311168
EST:     ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGG                         ACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT
genomic: ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGGgtaagttgat ... aaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT
EST: gi|6719881|gb|AW307528.1|AW307528
EST:     ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGG                         ACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT
genomic: ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGGgtaagttgat ... aaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT
EST: gi|193384803|gb|FK353161.1|FK353161
EST:     ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGG                         ACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT
genomic: ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGGgtaagttgat ... aaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT
EST: gi|254323159|gb|GR835767.1|GR835767
EST:     ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGG                         ACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT
genomic: ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGGgtaagttgat ... aaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT
EST: gi|193422220|gb|FK389679.1|FK389679
EST:     ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGG                         AACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTT
genomic: ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGGgtaagttgat ... aaaattgcagA-CAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTT
EST: gi|254323158|gb|GR835766.1|GR835766
EST:     ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGG                         ACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT
genomic: ATTATTATAGTTTGATTTCTTTGAAGACAATTGCAATTTGCATTATGGGGgtaagttgat ... aaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctttttattatctatgagttacttaataagctcatatttatcaaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTTGTTAGGATTGATGAAGTGCTTTCCAGCCTTAAAGGAAAGCCATCGGAAG
                       acttaat  putative branch site (score: 4)
     ttttattatctatgag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaatcaaatatatcatttaaaaattgtggtggctctggattctctcctttttattatctatgagttacttaataagctcatatttatcaaaattgcagACAAAAATCATCCCTTCTAAATACATCATGAAAACAGATGATGATGCCTTTGTTAGGATTGATGAAGTGCTTTCCAGCCTTAAAGGAAAGCCATCGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - - ctctgga