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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatatcaaaattaatgtcacaattactatatataaacagatgtaaagaaaatatatactaactatgtacatccatctctattttaatgcactcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAG

Basic information

species Glycine max
transcript GLYMA19G01470.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------------------------------------------------acatatcaaaattaatgtca-caattactatatataaaca--gatgtaaagaaaatatatactaactatgtacatccatctctattttaatgcactcat-tcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAG
                                                                                                    | | |  |  ||| | | |  ||| | ||   |||||   || |        |||    ||| |||| | |      |  |  |   |    | || |||| || |  ||||  |  |   ||| |||||| | |||||  |||||| |||||| || || ||||| |||||||||||||| || |||||||||||||| |
gtaagcgaatatatcatcactattttctatttgtttagttttaggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatt-taccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgttttttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG

upper sequence: GLYMA19G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G100724_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------acatatcaaaattaatgtcacaattactatatataaa---cagatgtaaagaaaatatatactaac-tatgtacatccatctct--attttaatgcactcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAG
                                                                       | || |   ||  |  | |  |  | | ||| ||   |  |   |   |   | ||| ||||  |||| | |  ||  |    || ||  |  | |   |||| || |  || |  |  |   ||| |||||| | |||||  ||||||||||||| || || | ||| |||||||||||||| || |||||||||||||| |
gtaagagaagcatcactattattatcatctatttgtttagtttatatgaagaatttgatgttcttgatttctttccaccgtaccgataaagctgttgtttattaattaccaagacattaattttttatgctaaaatatgaagaaacaattaaaaatgttcttttaatatctcagGAAGAACATACCAACCTATCAGACGAAGAATTATATCGGTATGCCAGATTGGTCACTTCTGTTGTCATTGCAAAGGTTCACACTATTGATTGGACTGTCG

upper sequence: GLYMA19G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G312997_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------acatatcaaaattaatgtcacaattactatatataaacagatgtaaagaaaat---atatactaac-tatgtacatccatctctattttaatgcactcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAG
                                                                    | || |   ||  |  | |  |  | | ||| ||        |    |||    ||| ||||  |||| | |  ||  |  |  |            |||| || |  ||||  |  |   ||| |||||| | |||||  |||| |||||||| || || ||||| |||||||||||||| || |||||||||||||| |
gtaagagaagcatcgctattattatctatttatttagtttatatgaagaatttgatgttcttgatttctttccaccgtaccgataaagctgttttttattaattaccaagacattaattttttatgctaaaatatgaagaaacaattacaaatgtccttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGATATGCTAGATTGGTCACTTCTGCTGTCATTGCAAAGGTTCACACTATTGATTGGACTGTGG

upper sequence: GLYMA19G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0066g01670.t01 (Vitis vinifera), 3'ss of exon 5
acatatcaaaattaatgtcacaattactatatataaacagatgtaaagaaaatatatactaactatgtacatccatctctattttaatgcactcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAG
            || | | | |||| ||| ||||   |  | |     | | |||| |  |   |  || | |  |   | |  |  ||   |  |||||||  | |||   ||  ||   ||||||||||| ||||  | ||| ||  ||||||| || ||||| ||||||||  |||||||||| ||||||||||| |
--------gtgctattat-ataattgcta-atatgccctcaaggtgtcatattataaatgagtaaattaaaactttgattttggttttgtgatgtttcagAAGGAATATAGACATATGAACGATGAAGAACTGTATCATCGTGCAAGGCTGGTGACTTCTGCTGTAATTGCAAAAATTCATACCATAGATTGGACTGTGG

upper sequence: GLYMA19G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0066g01690.t01 (Vitis vinifera), 3'ss of exon 6
acatatcaaaattaatgtcacaattactatatataaacagatgtaaagaaaatatatactaactatgtacatccatct--ctattttaatgcactca----ttcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAG
   ||                |||||  ||| | | | | ||||| |     |||||  ||  |      ||  || |    | || |||   |  |    || ||||  |  ||   || ||| | ||||| ||||| || || ||||| ||  ||||||| || ||||| |||||||| |||| ||||||||||||||| || |
--gtacaccggccggccctttaattaggatacacatatatatgtatatttg-tatat-ttagatgctcttattaatttgatgaattcaatcttccaaatgttttagAAGGAAAATGGACATTTGAGCGATGAGGAACTGTACCGTCATGCAAGGCTGGTGACTTCTGCTGTAATTGCAAAAGTTCTTACCATTGATTGGACCGTGG

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|15663097|gb|BI700468.1|BI700468
EST:     GACAATCTCAAG                         AAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTG
genomic: GACAATCTCAAGgtgtgtgtat ... actcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTG
EST: gi|254336835|gb|GR843014.1|GR843014
EST:     TGCAGGCCCTTTTCATTCAAGAACACAATGCAGTTTGTGACAATCTCAAG                         AAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTG
genomic: TGCAGGCCCTTTTCATTCAAGAACACAATGCAGTTTGTGACAATCTCAAGgtgtgtgtat ... actcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTG
EST: gi|21889538|gb|BQ742751.1|BQ742751
EST:     TGCAGGCCCTTTTCATTCAAGAACACAATGCAGTTTGTGACAATCTCAAG                         AAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTG
genomic: TGCAGGCCCTTTTCATTCAAGAACACAATGCAGTTTGTGACAATCTCAAGgtgtgtgtat ... actcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTG
EST: gi|254347310|gb|GR853559.1|GR853559
EST:     TGCAGGCCCTTTTCATTCAAGA-CACAATGCAGTTTGTGACAATCTCAAG                         AAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGAT
genomic: TGCAGGCCCTTTTCATTCAAGAACACAATGCAGTTTGTGACAATCTCAAGgtgtgtgtat ... actcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaaatatatactaactatgtacatccatctctattttaatgcactcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAG
                                              ctcattc  CT-rich tract
     aatatatactaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatatcaaaattaatgtcacaattactatatataaacagatgtaaagaaaatatatactaactatgtacatccatctctattttaatgcactcattcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
-catatca
- - - - - - - -tgtcaca
- - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtac