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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttttttttaatctatttatttgtttatttttgggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacagcagACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCC

Basic information

species Glycine max
transcript GLYMA15G07570.3
intron # 3
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatccttttttttaatctatttatttgtttatttttg-ggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacagcagACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCC
||||||||||| | | |||  || |  |||| | |||  ||  |  | |||   ||  ||    |  |   |    | |||  |||||||| ||   |||||||| ||||||||||| || || || ||||| ||||||||||||||||| || ||||  || || || || ||||| ||||||||||| ||||| || ||   
gtatcctttttctgattctggttttgagtttttgtttatggaattggtgtgtttgatgtttagcttatctactccttttgaacttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA---

upper sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 8
gtatcctttttt---ttaatctatttatttgtttatttttgggtctatgagtgcaaga--gattgtattctttatccagctatga---ttttccttattgatctacagcagACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCC
|||||||||| |   ||    |      ||  || | ||   | |||  ||||       |     ||||  | |  |||| | |   || |||||||||||  | ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||  |||| || ||||| ||||||||||| ||||| ||||| || ||   
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA---

upper sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 6
gtatcctttttt---ttaatctatttatttgtttatttttgggtctatgagtgcaaga--gattgtattctttatccagctatga---ttttccttattgatctacagcagACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCC
|||||||||| |   ||    |      ||  || | ||   | |||  ||||       |     ||||  | |  |||| | |   || | |||||||||  | ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||  |||| || ||||| ||||||||||| ||||| ||||| || ||   
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcaatttttagctgtaaagcttattcttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA---

upper sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 3
lower sequence: PP1S268_9V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatccttttttttaat-ctatttatttgtttatttttgggtctatgagtgcaagagattgtattct-ttatccagctatgatt---ttccttattgatctacagcagACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCC
    |        | || ||| | ||  ||  | ||   ||  | ||  | |      |   ||||| |||    |   || |    |||||||  ||   |||||||||||||||||||  || || || || ||||||||||||  |||||| |||||  ||||  | || |||||||| || || ||||| |||||||| ||   
----ctgaacgaatgatgctaatgatcagtgaaattaaagggttgtgt-tactcattctgaaattctcttacagtgggctggtccaattccttagcgaggaacagCAGACATAGATCTTGGCACCATTACTGACCGCATGGCTGTTCGAAAGGCTGTACAGTGTGGACAGGTGGAAGATGCTATCGACAAAGTCAATGACTTGAA---

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|298181140|gb|HO022579.1|HO022579
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-
EST: gi|298181140|gb|HO022579.1|HO022579
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-
EST: gi|192297765|gb|FG989971.1|FG989971
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-
EST: gi|192297765|gb|FG989971.1|FG989971
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-
EST: gi|193719536|gb|FK650872.1|FK650872
EST:     CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCC                         A
genomic: CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAG-Cgtatcctttt ... tctacagcag-
EST: gi|193719536|gb|FK650872.1|FK650872
EST:     CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCC                         A
genomic: CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAG-Cgtatcctttt ... tctacagcag-
EST: gi|193719536|gb|FK650872.1|FK650872
EST:     CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCC                         A
genomic: CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAG-Cgtatcctttt ... tctacagcag-
EST: gi|8283127|gb|BE020688.1|BE020688
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAAC                         ACATAGCTCTTGCA
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcagACATAGATCTTGCA
EST: gi|15812571|gb|BI784846.1|BI784846
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCC                         A
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAG-Cgtatcctttt ... tctacagcag-
EST: gi|15812571|gb|BI784846.1|BI784846
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCC                         A
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAG-Cgtatcctttt ... tctacagcag-
EST: gi|15812571|gb|BI784846.1|BI784846
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCC                         A
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAG-Cgtatcctttt ... tctacagcag-
EST: gi|151408269|gb|EV278077.1|EV278077
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-
EST: gi|151408269|gb|EV278077.1|EV278077
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-
EST: gi|207765821|gb|GD735462.1|GD735462
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-
EST: gi|207765821|gb|GD735462.1|GD735462
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-
EST: gi|9819896|gb|BE555339.1|BE555339
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-
EST: gi|9819896|gb|BE555339.1|BE555339
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         C
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tctacagcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaagagattgtattctttatccagctatgattttccttattgatctacagcagACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCC
 ttccttatt  putative branch site 
        attgtattctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttttttttaatctatttatttgtttatttttgggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacagcagACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG