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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgccatccttaagtcaggaaatatggattgacaaaagtatacattattagtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA

Basic information

species Glycine max
transcript GLYMA14G37520.1
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 18
---gttagtgccatccttaagt-caggaaatatggattgacaaaagtatacattattagtgctcctgcacttactatctatatgt-tagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA
    | ||     |  |  |||       | ||   |     || |||   |||  ||  |    |||  | || ||   | | |  ||||||||||||| || ||||||||||||||  | || ||||||||||||| ||| |||||||| || |||||    ||||| ||||| |  ||
gtaatcaggaaagttttggagtatttcttacataactcttgcaaggtagttatttatatgggcgttgc-ttaacaattgttgtttgcagATACAATGGCGTGCTCTTGATGAGATAAACTCTGGGGTGTGTGATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
---------------gttagtgccatccttaagtcaggaaatatggattga--caaaagtatacattattagtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA
               |  | | |||  || |||| || |||| | |  | |      ||    ||    |    ||       || | || | |    |||||||||||||| ||||||||||| ||||| || ||  | |||||||||| ||| ||||| ||||| ||||| |  |  || || || || ||
gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
lower sequence: LOC_Os03g18310.3 (Oryza sativa), 3'ss of exon 16
---------------gttagtgccatccttaagtcaggaaatatggattga--caaaagtatacattattagtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA--------
               |  | | |||  || |||| || |||| | |  | |      ||    ||    |    ||       || | || | |    |||||||||||||| ||||||||||| ||||| || ||  | |||||||||| ||| ||||| ||||| ||||| |  |  || || || || ||        
gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAGTACGCAA

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
lower sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
------gttagtgccatccttaagtcag--gaaatatggattgacaaaagtatacattattagtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA
      | |    | ||     ||||     ||| |    |||  |      ||||  |  | |||||   |   |  ||| | ||     |||||||||||| || ||||||||||| ||| | || ||||||||||||| ||| |||||||| || ||||| | |||||| ||||| |  ||
gtatttggttacacgatttaggagtcttcttaaagaactgttgctatgtaagtacagcaagattgctcg-acttgtgttatttgta-----gATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
gttagtgccatccttaagtcaggaaatatggattgacaaaagtatacattatt------agtgctcctgcactta------ctatctatatgt-----tagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA
|||||  | ||| | | || |  ||||| ||  |  ||| | |   |  || |      |||| | |   |  ||       | ||   ||||     |||||||||||||| || ||||||||||| ||||| || || |||||||||| |||||| || ||||| ||||| |  |  || || || || ||
gttag--ctatcat-aggtgataaaata-ggcctagcaagactgctctctacttatagaagtgttaccaaaactaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 18
gttagtgccatccttaagtcaggaaatatggattgaca---aaagtatacattatt--------agtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA
||| |||    |||   ||| |  ||| |    ||||     | || || | ||||        ||     |      |  ||| |  || |||| | |||||||| || || || ||||| ||||| || || |||||||||| ||||||||||||  | ||||||||||||||||| || |||||
gttggtgtttacctactgtccg--aatgtcttctgactcttgaggtgtataatattttgttgcgaggaaatcgatttctcatattttcatcttagGTGCAATGGCGTGCCCTGGACGAGATCAATGCTGGAGTTTGTGATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGA

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 18
---------------------gttagtg--ccatccttaagtcaggaaatatggattgacaaaagtatacattattagtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA
                      || |||    | |   || ||  | ||| ||  | || |  |||||| |  |||       ||  |  |  | |   | || |||||||||||||| |||||||||||||||||||| || ||||||||||| | |||||||||||| || |||||||||||||| ||||| |||||
tagcttttgaatttagaaaaatttggtggataaccaacaaatctaggaatttgtgtggaaatgagtatagaaaatt-------ctataacttttttacttttggtagATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA

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|193519728|gb|FK476263.1|FK476263
EST:     CACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG                         ATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAG
genomic: CACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAGgttagtgcca ... tatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAG
EST: gi|213613561|gb|DB978638.1|DB978638
EST:     CACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGATAGGTTTCCAAAG                         ATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAG
genomic: CACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAGgttagtgcca ... tatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAG
EST: gi|193308294|gb|FK277299.1|FK277299
EST:     CACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG                         ATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAG
genomic: CACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAGgttagtgcca ... tatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattgacaaaagtatacattattagtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA
                                  cacttac  putative branch site (score: 2)
        aaaagtatacattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgccatccttaagtcaggaaatatggattgacaaaagtatacattattagtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG