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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcactcttggtttttttacaatactcattcagcttctctagtaaaaaggttaaacttatgatgctttactggacactgacattataacttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA

Basic information

species Glycine max
transcript GLYMA02G41890.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G41890.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 2
gtcactcttggtttttttacaatactcattcagcttctctagtaaaaaggttaaacttatgatgctttactggacactgacattataacttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA
           ||||  | ||| |    |||   |||  || |      | | |||| | | || |       | | | | |||  |  |  | |  ||||||| |||||||| ||||| |||||||| || || |||||||| || ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||
-----gtacaattttaatgcaacatcttttcc-tttcagtattttttttggtcaactga-ggtgatc------atatttatatttcatgtgatgt-cagGTTGTTGAGGATGGATATGAGTTCTTTGCCGACAGACAACTTGTCACCATATTCTCAGCTCCAAACTATTGTGGTGAATTTGATAATGCAGGTGCAATGA

upper sequence: GLYMA02G41890.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G160237_T02 (Zea mays), 3'ss of exon 3
--gtcactcttggtttttttacaatactcattcagcttctctagtaaaaaggttaaacttatgatgctttactggacactgacattataacttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA
    | |  | |  |||  | ||       ||  | |  | |  |   |  |||||    |   ||      |  | | || |||   |  |  | |  ||||||| ||||||||||||||||| |||||||| || || ||||| || ||||| || || || || ||||||||||||||||| ||||||||||| ||||
gtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattg-catgcgatgtgatgt-cagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATATTCTCGGCCCCCAATTATTGTGGTGAATTTGATAATGCTGGTGCAATGA

upper sequence: GLYMA02G41890.2 (Glycine max), 3'ss of exon 2
lower sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtcactcttggtttttttacaatactcattcagcttctctagtaaaaaggttaaacttatgatgctttactggacactgacattataacttttatg-tagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA
        | | | |||| ||||   |||   |  ||| |  ||  |  | |    || ||||| |       |||  |   ||  |  |||||||  |||| || |||||||||||||| |||||||||||||| |||||||| ||| | ||||||||||| ||||| |||||||||||||| ||||||||||||||||
-------gtagatatttttcaat---cat---gtctctttgatactactgct---tttgtgatgtt------aacaagggagttggattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA

upper sequence: GLYMA02G41890.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g02410.t01 (Vitis vinifera), 3'ss of exon 2
gtcactcttggtttttttacaatactcattcagcttctctagtaaaaaggttaaacttatgatgctt-tactggacactgacattataacttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA
                         | |||  || | | ||||        |     |||  | ||  | ||| | ||||| ||| |   |||  | |||||||| |||||||| |||||||||||||| |||||||||||||||||  |||| |||||||| ||||| |||||||||||||| ||||||||||| ||||
------------------------gttatt-ggcatttttagttttc--tcttgttctattttactcatgctgaaaactgaaattcttcttttggtctagGTTGTGGAGGATGGATATGAATTCTTTGCCGATAGGCAACTTGTTACCGTATTCTCAGCTCCCAACTACTGTGGTGAATTTGATAATGCTGGTGCAATGA

upper sequence: GLYMA02G41890.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S97_286V6.1 (Physcomitrella patens), 3'ss of exon 3
gtcactcttggtttttttacaatactcattcagcttctctagta--aaaaggttaaacttatgatgctttactggacactgacattataacttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA
| |    |||    |   |    | | |     ||  || |  |  | |   ||| | |  |  |    || ||   |      |   |  ||  ||  |||| ||||||||||| |||||||| || ||| |  | ||||| ||||| || ||||| |||||||| ||||||||||||||||| ||||| ||||| ||||
gacgaatttgaacctccgatgcgattgacatgtctcttccaccaccatacttttatattctttgtatacta-tgctgatctgtgtgggatgttacatacagGTAGTAGAGGATGGTTATGAATTTTTCGCTAAGCGCCAACTGGTTACCATTTTTTCTGCTCCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

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|17963355|gb|BM270105.1|BM270105
EST:     CTGAGTTCTTGACAAAGCATGACTTGGACCTCATTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATA
genomic: CTGAGTTCTTGACAAAGCATGACTTGGACCTCATTTGTCGTGCTCATCAGgtcactcttg ... ttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATA
EST: gi|6913619|gb|AW395149.1|AW395149
EST:     CTGAGTTCTTGACAAAGCATGACTTGGACCTCATTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATA
genomic: CTGAGTTCTTGACAAAGCATGACTTGGACCTCATTTGTCGTGCTCATCAGgtcactcttg ... ttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATA
EST: gi|14991799|gb|BI317472.1|BI317472
EST:     CTGAGTTCTTGACAAAGCATGACTTGGACCTCATTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATA
genomic: CTGAGTTCTTGACAAAGCATGACTTGGACCTCATTTGTCGTGCTCATCAGgtcactcttg ... ttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATA
EST: gi|207772753|gb|GD743947.1|GD743947
EST:     CTGAGTTCTTGACAAAGCATGACTTGGACCTCATTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATA
genomic: CTGAGTTCTTGACAAAGCATGACTTGGACCTCATTTGTCGTGCTCATCAGgtcactcttg ... ttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaggttaaacttatgatgctttactggacactgacattataacttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA
                                      ttataac  putative branch site (score: 2)
                                            cttttat  CT-rich tract
                                     attataacttttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcactcttggtttttttacaatactcattcagcttctctagtaaaaaggttaaacttatgatgctttactggacactgacattataacttttatgtagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG