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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaaggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG

Basic information

species Glycine max
transcript GLYMA12G14060.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G14060.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 2
gtatgtgaa-ggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
||| ||| |  | |      ||||     |  ||| |     || | | | | | ||||   |  |     || ||  |  | ||||         ||   | |||| |||||||| |||||| |  | |||||||||||| | ||  | || ||  |||| ||||||||||||||||| | ||||||||| ||||||||||| |
gtacgtgcatagatttgggctaagcatactttttacggtataatctcactaactgtgct---gattaagttctgttgctgtttcttt--------gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTCATCATAAATACTCCATGTGAATCAGCTCAGAAGTACTGGATTGGTGGAG

upper sequence: GLYMA12G14060.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtgaaggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
    ||     |       | | |   | ||||   | |     ||  | ||  || | || |    | |  || |    | || |  |      ||   |||||| || |||||||||||||| || ||||||||  |||| || |  || ||||| || |||||||| |||||||| | ||||||||||||||||||||| |
----gtaggcatattttcttgatt---gccattttttttctccatatgtcatggtgatcttccacatttatattga---gttctatttatttcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG

upper sequence: GLYMA12G14060.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G06310.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtgaaggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
                      || ||   |||       ||| |     ||| |       |  | |   | ||  | ||| ||       |   ||||  |||| || |||||||||||||| |||||||||||  |||  || |  || ||||| || |||||||| |||||||| | ||||||||||||||| ||||  |
----------------------gtaggcatattgcagtgtcattttg--catt-tatccagactatatatgtattggtgatctttgatttggtggctttc--agGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG

upper sequence: GLYMA12G14060.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtgaaggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttca---tagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
||||||||||||||    || | |||| |        | |    |  || || ||| | || | || || || ||  | |   ||    |  |  ||        |||||||||| ||||||||||| || || ||||| ||||| || || || ||||| || || | ||| |||||||| | ||||||||| ||||| || || |
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttctt-cattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG

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|16996251|gb|BM085623.1|BM085623
EST:     ATGATATCAAGGGTTGTTTTGCTATGTCGGAGTTAGGCCATGGAAGTAAT                         GTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTT
genomic: ATGATATCAAGGGTTGTTTTGCTATGTCGGAGTTAGGCCATGGAAGTAATgtatgtgaag ... attttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatgcttttgccttgtcacttttaataatcctttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
                                        gactaat  putative branch site (score: 2)
                                              ttttcat  CT-rich tract
                      ttttaataatccttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgaaggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG