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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaacctgtaaaaaatagatcttggtttgccacttgtttaaagaggcttttccctcctccccagtttctcgaaatgataaatcagattccttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC

Basic information

species Glycine max
transcript GLYMA12G06450.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06450.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
acaacctgtaaaaaatagatcttggtttgccacttgtttaaagaggc-ttttccctcctccccagtttctcgaaatgataaatcagattccttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC
 |  || | ||||  |  ||      ||   |  | | |         ||||   |  |     |||| |     |  |   | | |      |  | ||||| |||||||| ||||| ||||  || || |||||||| || || ||||| |||||||||||||| ||||| ||| |||| || || ||| | |||||||
-ccccccggaaaagttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC

upper sequence: GLYMA12G06450.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
acaacctgtaaaaaatagatcttggtttgccacttgtttaaagaggcttttccctcctccccagtttctcgaaatgataaatcagattcct-tatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC
  |  |||     | || |  || | ||    |||| ||  |  |     ||            |||| |    || |      | | | | |  ||  |||| |||||||||||||| |||||||| || |||||||||||||||||||| ||||||||||| || ||||| ||||||||  | ||||||||||||||||
-gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC

upper sequence: GLYMA12G06450.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------acaacctgtaaaaaatagatcttggtttgccact-tgtttaaagag----gcttttccctcctccccagtttctcgaa-----------------------atgataaat------cagat------tccttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC
                                          |  ||  |   || || |||| | | | | |  |||    |||    | | ||| |||     | || |    |                        ||| | |||      | |||      | ||  ||| ||||| |||||||| || || ||||||||||||||||| || |||||  ||||||| ||||||||    || || |||||| | |||  |||||||   || |
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC

upper sequence: GLYMA12G06450.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S35_216V6.1 (Physcomitrella patens), 3'ss of exon 9
acaacctgtaa--aaaatagatcttggtttgccacttgtttaaagaggcttttccctcctccccagtttctcgaaatgataaatcagattccttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC
   |  ||||         ||   || ||||     || | || |   |  ||   |||        |    | |     |  |  | |    |  || ||||| ||||||||||| || |||||||| ||||| || || |||||| ||||||| ||||||||    || ||||||||| | ||    || |||  |||||
-ggatttgtacctgtggaggaagctgatttgtgttatggtgaatgcctcaattgtttccggtatgcgtatgagtagcctgatgttcggtgatgtg-atgcagGCAATGATGAAAGACCAGTTTGCAAACTACGTGGTCCAGAAGGTGTTGGAAACCTGTGATGAATCTCAACGCGAGCTGTTGCTGGGTCGTATTCGGGTTC

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|193436590|gb|FK402084.1|FK402084
EST:     TACTAGTGAGTCAGATGCTTGGCACCACAGATGAAAACGAACCTCTTCAG                         GCGATGATGAAAGATACAAATTTGCAAATTACGTT
genomic: TACTAGTGAGTCAGATGCTTGGCACCACAGATGAAAACGAACCTCTTCAGgtttgttgaa ... ttatatacagGCGATGATGAAAGAT-CAA-TTTGCAAATTACGTT
EST: gi|15204205|gb|BI426973.1|BI426973
EST:     TACTAGTGAGTCAGATGCTTGGCACCACAGATGAAAACGAACCTCTTCAG                         GCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAA
genomic: TACTAGTGAGTCAGATGCTTGGCACCACAGATGAAAACGAACCTCTTCAGgtttgttgaa ... ttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAA
EST: gi|193519741|gb|FK475828.1|FK475828
EST:     TACTAGTGAGTCAGATGCTTGGCACCACAGATGAAAACGAACCTCTTCAG                         GCGATGATGAAAGATCAATTTGCA
genomic: TACTAGTGAGTCAGATGCTTGGCACCACAGATGAAAACGAACCTCTTCAGgtttgttgaa ... ttatatacagGCGATGATGAAAGATCAATTTGCA
EST: gi|213591020|gb|DB973775.1|DB973775
EST:     TACTAGTGAGTCAGATGCTTGGCACCACAGATGAAAACGAACCTCTTCAG                         GCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAA
genomic: TACTAGTGAGTCAGATGCTTGGCACCACAGATGAAAACGAACCTCTTCAGgtttgttgaa ... ttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttccctcctccccagtttctcgaaatgataaatcagattccttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC
                                         ttccttat  CT-rich tract
                          aaatgataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaacctgtaaaaaatagatcttggtttgccacttgtttaaagaggcttttccctcctccccagtttctcgaaatgataaatcagattccttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT