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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaattgttttccgtttatcttctgtctgttgttgagactgatgagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA

Basic information

species Selaginella moellendorffii
transcript EFJ11911
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 7
----------------------------------gtacaattgttttccgtttatcttctgtctgttgttgagactgatgagttt--ctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                                  | | ||   |||  | || |   |   ||  |  |     ||    | | |  |  |    |  || ||   |  || || || ||||| || |||||||| |||||||| || ||||||||||| ||||| ||||||||  | ||||||||||||||||| || |
agtgcagttttctattctgttattgctgtatgctgaataacattttgacattcacacttcttccttaatattatctatctaatataacaatttattatagAGTTCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAACATGGAGACAGCACAATTTTTCAAGCGTGATTTTGAGGAAAATGGTTCAA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 7
--------------------------gtacaattgttttccgtttatcttctgtctgttgttgagac----------tgatgagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                          || || || ||| |       | | | |   | | |||  |          || ||| |   |||  | ||||| ||| ||  || ||||||||||| ||||| ||||| |||||||| ||||| ||||| || || || || |||||| | |||||||| || || || || |
atggtatgctgtagagcaatttacctgttcatttttttccatggagacatttttgcatcgctgaatcactgcttatttgctgattacttttaatctccagGGTGGTGAAGATGACAACTTTGCTATCGTGTTTGCTGCTATGGGAGTGAATATGGAAACAGCCCAATTCTTCAAACGTGATTTTGAAGAGAACGGGTCAA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 7
---------------------------------gtacaattgttttccgtttatcttctgtctgttgttgag--actgat--gagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                                 |||  | ||| | |  |  || | ||   | | | | |   |||| |     ||| | |    | ||| ||| ||  || ||||||||||| || || ||||| |||||||| ||||||||||| || || || || |||||| | |||||||| || ||||| || |
tactgtaaggtcaacattcatatggagcattgtgtattaatgtatgctttacatgt-ctaaatatggcttaatcactgcttctgatttttgtaacctgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 7
------------------------gtacaattgt---tttccgtttatcttctgtctgttgttgagactga---------tgagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                        | |  |||||   ||   || |   ||   | | ||  | || || |         |  | || | |    | ||| ||| ||  || ||||||||||| || || ||||| |||||||| ||||||||||| || || || || |||||| | |||||||| || || || || |
ttcctgtgaggtcaacatttatatggaggattgtgtattcatgtatgctttacatgtcttaataaggcttagtcactggttctgattttattacctgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 7
-----------------------gtacaattgtt---ttccgtttatcttctgtctgttgttgagactgatg---------agtttctttcgtatccagCGTGATGTTGAAG---ACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                        | || || ||       |||  | | |  |  | ||  || | || |          | |||  |   ||| ||| |||  |  ||||   |||| ||||| || || |||||||||||||| || ||||||||||||||||||||||||||| | || |||||||||||||| ||  
attaataagcctattttcttcttattcatttattggaacttgttactttacactaagatgaagaaagtggtttttccatctaattttgtcaatatacaggGTGGAGGAGAAGAGGACAATTTTGCCATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAAAATGGCTC--

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
------------------------gtacaattgttt---tccgtttatcttctgtctgttgttgagactgat---------gagtttctttcgtatccagCGTGATGTTGAA---GACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                         | || || ||       | |  | | |     | ||  || | ||||         ||  ||  |   ||| ||| |||  |  |||   ||||| ||||| ||||| |||||||||||||| || ||||||||||||||||||||||||||| | || |||||||| ||||| |   
aattaataaggctattttcttcttattcatttattggaacttgctactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT---

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 7
----------------------gtacaattgttttccgtttatcttctgtctgtt-gttgagactgat------gagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                       |||     || |    || | | || | |||  | ||| | ||||       |  | |  |  ||| ||| |||  |  || ||||| ||||| || || |||||||||||||| || ||||||||||||||||||||||||||| | || |||||||| |||||||| |
gtatagctgactgcttaatcatttacttaaattctttacttctgtactttttgtaagatgaaagtgatttttcaaaaataccatgttatgcagGGTGGAGAAGAGGACAATTTTGCTATTGTATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
------------------------gtacaattgttttc-----cgtttatcttctgt-ctgttgttgagactgatg-agtttctttcg-----tatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                        |   ||| |||| |     |  |   ||||||| ||  |  | |||   | | | ||| |  |      |||  || |||  |  || ||||| ||||| || || |||||||||||||| || ||||||||||||||||||||||||||  | || |||||||| |||||||| |
cttatttccttcagatttatttttgcttaatcgtttacttaaactctctacttctgtacttcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------gtacaattgttttccgtttatcttctgtctgttgttgagactg----atgagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                                    |  |   || | || ||  || ||| || | |  | |||     || |   |  |   | |||||  | |||  || ||||| |||||||| || ||||||||||||||||| ||||||||||| || |||||||||||  | |||||||| |||||||||||||
tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttt-tgtttgctttgtaaactccattattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------gtacaattgttttccgt-ttatcttctgtctgttgttgagactgatgagtttctttcgtat----ccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                                 ||| |  | |||    ||  ||      |  | |  ||  |  |   |   | | || |    ||||  | |||  || ||||| |||||||| || ||||||||||||||||||||||||||||| || ||||| |||||  | |||||||| ||||||||||| |
agttgttgtcaaaattgaatttcttgtttgtagacattcctcttcaacgttggctgtctcataatatcaaggattctttctcattcttgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTGTTTGCAGCTATGGGTGTGAACATGGAGACAGCTCAGTTCTTCAAGCGAGATTTTGAAGAAAATGGATCAA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
---------------------------------gtacaattgttttccgtttatcttctgtctgttgttg--agactgatgagtttctttcg-tatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                                 |||    |||  | |  | || |  | |       |   | | || |   ||| | |   | | |||| | | |  || || ||||| || || || || ||||| |||||||||||||||||||||||||| ||||| ||| | ||||| ||||| ||||||||||
ctcctttgatttggtaaaatctacaatgagttggtagttgtgtaatgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------gtacaattgttttccgtttatcttctgtctg-ttgttgagactgatgagtttctt--tcgtatccagCGTGATGTTGAA---GACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                               |  | ||  ||||  ||||||   | |    ||| |  ||   || | |||  |  |  || |  ||  ||||| |||   ||||||||||| || || |||||||||||||| || ||||||||||||||||||||||| ||| | ||||| |||||||||||||| |
gatgttaaatgaccatttatttcctttttattttattttctttctttttatcaattttgaacttgctatgagatatcatttttctacttttaacttgcagGATGTGGAAGAGGACAACTTTGCCATTGTTTTTGCAGCTATGGGAGTAAACATGGAGACTGCACAGTTTTTTAAACGTGATTTCGAGGAAAATGGATCAA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------gtacaattgttttccgtttatcttctgtctgttgttgagactgatgagttt------------ctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                            ||   ||||||   ||| |||| | ||||   || | |    | | | |            |||  || |  ||  ||| || || ||||| || || ||||||||||| |||||||| || |||||||| || ||||| ||||| ||  | |||||||||||||||||||| |
ccgttcatttctgtcctaccctttgtccacttctgttttatatttttcttttatctg--attaaaatatgtaattctcatattatttgccttgagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA

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|169049346|gb|FE458244.1|FE458244
EST:     GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTGGAG                         CGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
genomic: GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAGgtacaattgt ... tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
EST: gi|169092669|gb|FE496263.1|FE496263
EST:     GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAG                         CGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
genomic: GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAGgtacaattgt ... tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
EST: gi|169035381|gb|FE444319.1|FE444319
EST:     GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAG                         CGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
genomic: GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAGgtacaattgt ... tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
EST: gi|169036846|gb|FE443832.1|FE443832
EST:     GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAG                         CGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
genomic: GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAGgtacaattgt ... tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
EST: gi|169049517|gb|FE458740.1|FE458740
EST:     GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAG                         CGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
genomic: GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAGgtacaattgt ... tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
EST: gi|169059085|gb|FE468230.1|FE468230
EST:     GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAG                         CGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
genomic: GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAGgtacaattgt ... tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
EST: gi|169088665|gb|FE491525.1|FE491525
EST:     GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTGGAG                         CGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
genomic: GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAGgtacaattgt ... tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
EST: gi|169057426|gb|FE465730.1|FE465730
EST:     GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTGGAG                         CGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC
genomic: GCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAGgtacaattgt ... tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAAC

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), 35 (downstream exon)
Score: 45

ACTTTTCTCGGCTGCTGGGCTGTCGCACAACGAAATTGCTGCTCAAATATGCCGACAAGCCGGACTTGTGAGACACTTGGACGCGGGGAACGTTTTAGAGgtacaattgt ... tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccgtttatcttctgtctgttgttgagactgatgagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
                             gactgat  putative branch site (score: 45)
                                       tttctttcgtatcc  putative PPT
       tttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaattgttttccgtttatcttctgtctgttgttgagactgatgagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA