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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttctgaaagactttgagatgaacaactagtcttgtatgatttctgttgcaataatcttctttaaatgtggacatgaacatgaggtcatttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGTTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA

Basic information

species Glycine max
transcript GLYMA15G05800.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G05800.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
--aacttctgaaagactttgagatgaacaactagtcttgtatgatttctgttgcaataatcttctttaaatgtggacatgaacatgaggtcatttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGTTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA
   |   |       ||      |    |  |  ||| || |    || |    |  | ||       | ||   | ||     | |  |   |   ||||||||||||| || ||||| ||| |||| ||||||||||||||||| || || ||||| || |||||||| ||||| || || || |||||| | |||||||
atgagaacatgcgtgctcgatcttaggtatttcctctggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatg--tgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA

upper sequence: GLYMA15G05800.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
aacttctgaaagactttgagatgaacaactagtcttgtatgatttctgttgcaataatcttctttaaa----tgtggacatg---aacatgaggtcatttgc---tgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGTTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA
          |||    || |||      |  | ||  ||   || |  | | || |||   |  | |    | || || |     |  |||||  |  |       ||||| ||||| || ||||| ||| |||| |||||||| |||||| | || || ||||| || || ||||||||||| ||||| || |||||| |||| ||||
----------agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA

upper sequence: GLYMA15G05800.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
aacttctgaaagactttgagatgaacaactagtctt--gtatgatttctgttgcaata-atcttctttaaatgtggacatgaacatgaggtcatttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGTTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA
   || | |||  ||||        |   |  | |   ||  |  ||  | | || || || | | |  | |     |      | | |||   | | | ||||||||||| || ||||| || ||||| ||| | ||||||||||| ||||| |||||||| || ||||||||||| ||||| ||||||||| |||| || |
---ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA

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|151400806|gb|EV270620.1|EV270620
EST:     CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAG                         GCA-TGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTG
genomic: CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtactaaact ... tttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTG
EST: gi|208121820|gb|GD918549.1|GD918549
EST:     GGTGTTCTAATGGTTGAG                         GCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGC
genomic: GGTGTTCTAATGGTCGAGgtactaaact ... tttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
EST: gi|192315816|gb|FK008526.1|FK008526
EST:     CTGGACATTTTCCAGGAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAG                         GCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
genomic: CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtactaaact ... tttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
EST: gi|16277896|gb|BI942619.1|BI942619
EST:     CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAG                         GCAATGGCACAAGTTGGTGGTTTG
genomic: CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtactaaact ... tttgctgcagGCAATGGCACAAGTTGGTGGTTTG
EST: gi|192315817|gb|FK008527.1|FK008527
EST:     TGGACATTTTCCAGGAAAG-CCAATCATGCCTGGTGTTCTAATGGTCGAG                         GCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAG-T
genomic: TGGACATTTTCCAG-AAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtactaaact ... tttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
EST: gi|51344848|gb|CO985581.1|CO985581
EST:     CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAG                         GCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
genomic: CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtactaaact ... tttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
EST: gi|31310977|gb|CD396180.1|CD396180
EST:     CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAG                         GCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
genomic: CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtactaaact ... tttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
EST: gi|31464579|gb|CD406607.1|CD406607
EST:     CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAG                         GCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
genomic: CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtactaaact ... tttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
EST: gi|192333875|gb|FK025136.1|FK025136
EST:     CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAG                         GCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT
genomic: CTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtactaaact ... tttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgcaataatcttctttaaatgtggacatgaacatgaggtcatttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGTTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA
       aataatcttctttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttctgaaagactttgagatgaacaactagtcttgtatgatttctgttgcaataatcttctttaaatgtggacatgaacatgaggtcatttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGTTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
-acttctg
- - - - - -gactttg
- - - - - - - - - - - gaacaac
- - - - - - - - - - - - - - - - - -tgtatga
- - - - - - - - - - - - - - - - - - - - - - -ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaac