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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA

Basic information

species Selaginella moellendorffii
transcript EFJ37436
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------gtacgctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
                                           ||| | ||||   || |||       |  |    ||   |  ||  || ||  | ||||   |||||||| ||||| ||||||||||| |||||||| ||||| |||||||| || ||||| |||||||| || || || 
tctgttggtcgacaccttttgcttggttatctagaattatttttactc-agcttttctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG

upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G033626_T04 (Zea mays), 3'ss of exon 2
-------------------------------------------gtacgctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA------------------
                                            ||    || || | | || |  | | | |   | |       ||     ||  | ||||   |||||||||||||| ||||| || || |||||||| || || ||||||||||| || || || ||||| || |||||                   
tgtggaaaacccactagcattcatagtattaatcaatattgttttaactcagttatattctgta--ggaaaacaaatatgtgatatttccccccttttgcagGCCAGAAATGGTTGTAGGTTGGTATCACTCACATCCTGGCTTCGGATGCTGGCTATCAGGCGTCGATATCAATACTCAGCAGGTCTATGCAAATCCACTT

upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G388576_T01 (Zea mays), 3'ss of exon 6
------------------------------------------gtacgctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
                                           ||    || || | | || |  | | | |  || |       ||     ||  |  |||   |||||||||||||| ||||| || || |||||||| || || ||||||||||| || || || ||||| || ||||| 
gttcatggagatctagcattcatagtattaatcaatattgttttaactcagttatattctgta--ggaaaacaagtatgtgatatttccccccttttgtagGCCAGAAATGGTTGTAGGTTGGTATCACTCACATCCTGGCTTCGGATGCTGGCTATCAGGCGTCGATATCAATACTCAGCAG

upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G033626_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------gtacgctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
                                            ||    || || | | || |  | | | |   | |       ||     ||  | ||||   |||||||||||||| ||||| || || |||||||| || || ||||||||||| || || || ||||| || ||||| 
tgtggaaaacccactagcattcatagtattaatcaatattgttttaactcagttatattctgta--ggaaaacaaatatgtgatatttccccccttttgcagGCCAGAAATGGTTGTAGGTTGGTATCACTCACATCCTGGCTTCGGATGCTGGCTATCAGGCGTCGATATCAATACTCAGCAG

upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G467059_T03 (Zea mays), 3'ss of exon 2
-----------------------------------gtacgctagctaaact---ttggattgaacacctcgttttctcagattattttctactc---cagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
                                    |    || ||    |   ||   | | | | |  || |  | ||||| |||||  ||    ||||   |||||||||||||| ||||| || || |||||||| || || ||||||||||| || || || ||||| || ||||| 
acagactcacttgcatctgtagtattaatgaataattgttttaactctgttgtattctgtaggaaaacaagtatgttgagatttttttccccttttacagGCCAGAAATGGTTGTAGGCTGGTATCACTCACATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG

upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA13G29660.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------gtacgctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
                                                                 ||   | |       || | ||    |  || ||      | ||| ||  |  | |||    ||||||||||| || ||||||||||| |||||||| |||||||| ||||| || || || |||||||| || ||||| 
gtatttttttatattattattattattattattattattattattattattattattattattattattattgtgttggatttggtttgttagttcattgatgttggttacttg-tgttgcagACCAGAAATGGTTGTTGGTTGGTACCATTCCCATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG

upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA15G09410.2 (Glycine max), 3'ss of exon 1
---------------------------gtacgctagctaaactttggattgaacacctcgttttctca--gattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
                            |    ||  |     |||||||       |   ||  |    | |   ||| |  | |||    || |||||||| || ||||||||||| |||||||| |||||||| ||||| || || || |||||||| || ||||| 
gtattttatttattatttgcgtatttatttttataattttgtgttggatttggtttattagttcattgatgttggatttgtgttgcagACCAGAGATGGTTGTTGGCTGGTACCATTCGCATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG

upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv18s0001g10820.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------gtacgctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
                                            | | || | |  || || ||||||      | |||||||   ||   | || || |||   ||| ||||| ||||||||||||||||| |||||||| |||||||||||||| || || || ||||| ||||| || || 
gaatatgcatatgctagacaccaatgtatgtagatatagacagatgc-ctggttccacctttgattgagt-tagctttttctcgtgtttggtgctgctgcagACCTGAGATGGTGGTAGGATGGTACCATTCACATCCTGGATTTGGCTGCTGGCTCTCTGGTGTGGACATTAACACACAACAG

upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S181_105V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------gtacgctagctaaactttggattgaac----acctcgtttt---ctcagattattttctac----tccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
                               | | |    | |||| || ||   |     |   || | |    | | |||  ||| | |    | ||||   ||||||||||| || ||||| ||||| ||||| |||||||| |||||| |||| || || || || || || || || 
gttgaatgtgtgagtgtcagttgtgaataaattctcagatttaactatgaatcatatctagattccggtgtgcatttaaattgctttgtgcacttttcagGCCAGAAATGGTTGTGGGCTGGTATCATTCACATCCAGGTTTTGGTTGCTGGTTATCTGGTGTGGATATAAATACTCAACAG

upper sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------gtacgc---tagctaaact-ttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
                                       |||||    |  ||||| |  | ||   | ||||| | |  ||  | |  || | | || |||    || ||||| || || ||||||||||||||||| |||||||| |||||| | || || || || ||||| || ||||| 
ctacttatatttgattcatgcgtaaactgaacgtgatgtgtacgaatatgtctaaaatactaga--aatcaccttgatgcctgtgttgtttgtgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG

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: 33 (upstream exon), 35 (downstream exon)
Score: 14

ACGTCTTTGCGATGCCTCAGAGCGGTACTGGCGTGAGTGTGGAGGCCGTGGATCCAGTGTTCCAGACTAAGATGATGGACATGCTGAAGCAAACAGGACGgtacgctagc ... tctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA
   agctaaa  putative branch site (score: 14)
                                       ttattttctactcc  putative PPT
                                      attattttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT