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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG

Basic information

species Selaginella moellendorffii
transcript EFJ28889
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 12
---------------------gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                     ||    |  ||  ||  ||   || || |     |||   ||   |   |||    |  ||||||||||||||| |||||||||||  |||| ||||||||||||    |||||||| |||||||||| ||||||||||| ||||| ||||| || || || |
gtaatttgccttgattacactgtcgctggagcctcgcattgtcatcgcctatcttctggagctaa-gaaatttctctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATCAACATGGACGCTGATGTGATCACCATCGAGAACTCCCGGTCCGACG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 13
----------------------------gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                            |||              |  | |    |  || ||| | ||||       ||    || |||||| |||||||| |||||||||||  |||| ||||||||||||    |||||||  |||||||||||||||||||||| ||||| ||||| || || || |
gtaatctttcttccatcagactgtcactgtaggctttcaatatcatcaccaatcttctgtaacttaaactga-acaactttctctcgacagATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATAAACATGGACGCCGATGTGATCACCATCGAGAACTCCCGGTCCGACG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G165747_T02 (Zea mays), 3'ss of exon 13
----------------------------------------------gtaaaa-gacgcgacgag--tttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                                               ||| |     | | ||    |    |||  ||   |||||      | || |||    |  | |||||||||||||||||||||||||| |||| ||||||||||||    ||||||||||||||||||| ||||||||||| ||||| ||||| || || || |
gtattagccttgaactatttttttcgaaaggaagccttgaactattttaagacagtaccatgaaacctgtgttaggatccctactgattgcc-ctttttttttcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G112149_T03 (Zea mays), 3'ss of exon 13
-------------------gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcg-ttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                    |   |||  |    | | | | |   ||  | |     |||| ||     ||    |  | ||||||||||||| |||||||||||| |||| ||||||||||||    |||||||||||||||| |||||||||||||||||||| ||||| || || || |
gtatattagccttgaaatgttttgagatacctgaaatctgtct---tttataatctctactgacggccccttttcttggatagATCCACACCCACATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGATGCCGATGTGATCACGATCGAGAACTCCCGGTCTGACG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G149751_T06 (Zea mays), 3'ss of exon 10
----------------------------------------gtaaaagacgcgacgagtttctatagcttcgtgactg-acactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                                        ||   ||| |   |        ||  ||| |  |||  | ||||   |  ||     |   |||||||||||||| |||||||||||| |||| ||||||||||||    | ||||||||||||||||| || |||||||| || || ||||| || || || |
gtcattctcttgaactgtgcgctgtggagcccttgccagtgtgggagaggtt-cacaccaacatttctttggcactccaaactgatttccttctg--ttggcagATCCACACCCACATGTGCTACTCCAACTTCAACGACATCATCCACTCGATCATCGACATGGACGCGGACGTGATCACCATTGAGAACTCGCGGTCCGACG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA19G29180.2 (Glycine max), 3'ss of exon 11
----------------------gtaaaagacgcgacgagtttctatagcttcgt----gactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                       |   |  |   |    ||| |  | | || |       ||  |    |    ||| | ||  ||||||||||||||| |||||||||||| |||| ||||||||||||    ||||||||||||||||||| ||||| ||||| || || ||||||||||| ||||
gtactttcggatcatcacaaatctctgaatcataatttcttttttcatcctcattttcacatgtaataatcaacttttcatattgacagATCCACACCCACATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCTGATGTTATCACCATTGAGAACTCTCGCTCCGATG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA16G04240.1 (Glycine max), 3'ss of exon 11
--------------------gtaaaagacgcgacgag---tttctatagct--tcgtgactgacactggcgttgt------------ttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                    | |||  ||   |  ||   ||| | | | |  || | | |  |||    |||||            ||   ||  |||||||||||| || |||||||||||  |||| ||||||||||||    ||||||||||||||||||||||||| ||||| || || ||||||||||| || |
gtacactcttttggatcatcgcaaatcactgaattagaaattttttttgttcatcctcattttcacatatgttgtaataatcaacttttcgtattgacagATCCACACTCACATGTGCTACTCGAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCCGATGTTATCACCATTGAGAACTCTCGCTCCGACG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA17G24400.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------------------------------------gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                                                                                  |    |||    | |  |||  ||       | |      |||   || ||   |||  ||||||||||||||| |||||||||||  |||| || |||||||||    | ||||| || ||||| || ||||||||||| || |||||||||||||| || |
gtacttctcatggattacaaaaaatcaatgcatttttttatcgtaggaattgagtatagtaccaaagggtttacaaatcaacgggttagatagaatgcatttacatcaaaatataatattttctg-tattcttaacaattgacagATCCACACCCACATGTGCTACTCTAACTTCAATGACATCATCCACTCAATCATTGATATGGATGCTGATGTGATCACCATTGAAAACTCTCGCTCTGACG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA17G23730.1 (Glycine max), 3'ss of exon 10
----------------------------------------------------------------------------------gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                                                                                  |    |||    | |  |||  ||       | |      |||   || ||   |||  ||||||||||||||| |||||||||||  |||| || |||||||||    | ||||| || ||||| || ||||||||||| || |||||||||||||| || |
gtacttctcatggattacaaaaaatcaatgcatttttttatcgtaggaattgagtatagtaccaaagggtttacaaatcaacgagttagatagaatgcatttacatcaaaatataatattttctg-tattcttaacaattgacagATCCACACCCACATGTGCTACTCTAACTTCAATGACATCATCCACTCAATCATTGATATGGATGCTGATGTGATCACCATTGAAAACTCTCGCTCTGACG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 11
------------------------------------------------------------------------------------------------------------------------------------gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtt--tgaaatcca--cagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                                                                                                                                       ||| |   || ||| |   ||   |||       ||  |   ||| ||  || | | ||  |||||||||||||| |||||||||||  | || ||||||||||||    | || || || ||||| || ||||||||||| || || ||||| || || ||||
gtatttgtatttcactttattgctccttcccacttaaagaatgttttttacgagtatgttgaccataatgtggtttctgccattttcgtggacaatagaatgtgatatcaagatgaaggacgtgaaacaattactaaataaaggaagagatctaatttattcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv08s0056g01570.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtaaaagacgcgacgagtttctatagcttcgtgact---gacactggcgttgtttgaaat----ccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
               ||    |    | |||| ||  |||  | |||   | |||||   |  |   |  |      ||||||||||||||| |||||||||||  |||| || ||||| |||    ||||||| ||||||||||| ||||||||||| || || ||||| || || ||||
gttctttcctcactgaattttctttcattttccatttcttgttcactttggccactgagctcatcctaggtaatatgacagATCCACACCCACATGTGCTACTCTAACTTCAATGACATTATCCACTCCATCATTGACATGGACGCTGATGTGATCACAATTGAGAACTCCCGATCTGATG

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|169057671|gb|FE463722.1|FE463722
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169060119|gb|FE468105.1|FE468105
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169109743|gb|FE511814.1|FE511814
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169101347|gb|FE502516.1|FE502516
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCCACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169103370|gb|FE507542.1|FE507542
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169030928|gb|FE440328.1|FE440328
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169061438|gb|FE469537.1|FE469537
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169032657|gb|FE436930.1|FE436930
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169022654|gb|FE429707.1|FE429707
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169022653|gb|FE429706.1|FE429706
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169027728|gb|FE434865.1|FE434865
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169053882|gb|FE460973.1|FE460973
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC
EST: gi|169101346|gb|FE502515.1|FE502515
EST:     CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACAACTCAG                         ATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATC
genomic: CCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 34 (downstream exon)
Score: 66

AGAGGGTCTTCCTCTCCGCAAGTCCGAGCAGGCCGCCTACTTGAACTGGGCCGTCCATGGTTTCCGCATCACGTCGTGCGGAGTGAAAGACACGACTCAGgtaaaagacg ... aaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcgacgagtttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
                        gactgac  putative branch site (score: 66)
         tttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA