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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcagttgtttagagcaatgcaatgcctcgctcggtctgatcttgtttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA

Basic information

species Selaginella moellendorffii
transcript EFJ26861
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 6
--------------------------gtaagttctcagttgtttagagcaa---tgcaatgcctcgct---cggtctgatct-tgtttaaaccaac-cagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                          ||| ||    | || | ||| | ||   |   ||  ||||      |||   || | ||  |  |   |  |||||||||| ||||| || ||||| || |||||| | || |||||||||||||||||  ||||||| ||||||||||||||||||| |||||||||| |  |
tagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcagGCACGCAGGAGGAGGCGGCGGAGGCGTACGACGTGGCGGCGATCAAGTTCCGGGGGCTCAACGCCGTCACCAACTTCGACATCACCCGCTACGACGTCGA

upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os03g07940.1 (Oryza sativa), 3'ss of exon 8
----------------------------------gtaagttctcagttgtttagagcaatgcaatgcctcgctcggtctgatcttgtttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                                  | |  || |    | |      |     |  |  | |     |   | |  | | | |||   |||||||||| |||||||| ||||| || |||||||| || |||||||||||||| ||| | ||||| || ||||||||||||||||||   |||||| | ||
aagtgaatatattgtgtcagaccaaattacttttggatatttttgcctatcgttttctggatatggtttggtgaattgaaaacgcggtgacaccgcgcagGCACGCAGGAGGAAGCGGCGGAGGCGTACGACATAGCGGCGATCAAGTTCCGCGGCCTGAACGCCGTGACCAACTTCGACATCAGCAAGTACGACGTGAA

upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 7
-------------------------------gtaagttctcagttgtttagagcaatgcaatgcctcgctcggtctgatc--ttgtttaaaccaac-cagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                               | |  ||     |  || |  |  |   | | | |||    || ||||   |||| |      |  |||||||||| ||||| || ||||| || |||||| | || |||||||||||||||||  ||||||| |||||||||||||||||||   | |||||| |  |
tgaccgcgcgcggcggcggcggcgaaaactcggattttacttttgattgatggtgagtgagttcgtcgtcgtgtgtgattggttgtatttgtggatgcagGCACGCAGGAGGAGGCGGCGGAGGCGTACGACGTGGCGGCGATCAAGTTCCGGGGGCTCAACGCCGTCACCAACTTCGACATCACGAGGTACGACGTGGA

upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 8
---------------------------------gtaagttctcagttgt-ttagagcaatgcaatgcctcgctcggtctgatcttgtttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                                 |||    |    | |  |||   ||| | |  |  ||  | |||       | ||||  | |  ||||||| ||||| ||||| || || ||||||||||| || || ||||||||||| ||| | |||||||| || ||||| |||||||   | |||||| |  |
actttgcagtaggatctacattggtttttggatgtataaacaagatggccttattacaacggagcgtttccattggttaatctatttttatgcaatacagGCACTCAAGAAGAAGCAGCAGAGGCATACGACATTGCTGCCATCAAGTTCCGTGGCCTGAACGCGGTGACGAACTTTGACATCACAAGGTACGACGTGGA

upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G008234_T01 (Zea mays), 3'ss of exon 5
------------------------------gtaagttctcagttgtttagagcaat---gcaatgcctcgctcggtctgatcttgtttaaac-caaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                              |   |  | |   ||  | || |  |    |     ||  |   | |       ||    || |   |||||||||| ||||| |||||||| || |||||| |||| || ||||||||| ||||| ||||||| |||||||||||||||||||  ||||||||| |  |
tcgcatcgcacgcgctgggggccatctgctgcccgcccccctctgcctcgatctttctttccggttctgacgatggccatcaccgtcggcacgcgcgcagGCACGCAGGAGGAGGCCGCGGAGGCGTACGACGTCGCGGCCATCAAGTTCAGGGGCCTCAACGCCGTCACCAACTTCGACATCACGCGCTACGACGTCGA

upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G028151_T01 (Zea mays), 3'ss of exon 8
---------------------------------------gtaagttctcagttgtttagagcaatgcaatgcctcgctcggtctgatcttgtttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                                       | |  | |   || || | | ||  |  |  | || | |  | | |     ||||        ||||||| || ||||| || ||||| || |||||| | ||||||||||||||||| ||| ||| |||||||||||||||||||||||  || |||||| |  |
cgcgctttgcctgtttgtttgaccgcgctgcccgaaagcgcatttccgacgtcgtgtcg-gcgtttaagcggct-gttaaggcgggagccgttttggtg---cagGCACCCAGGAGGAGGCGGCGGAGGCGTACGACGTGGCCGCGATCAAGTTCCGCGGCCTCAGCGCGGTCACCAACTTCGACATCACGCGGTACGACGTGGA

upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 7
-------------------------------gtaagttct--cagttgtttagagcaatgcaatgcctcgct-cggtctgatcttgtttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                                || ||          | | ||   |||    |    | |  | | ||||   || |  |   |  |||  || ||||| ||||| || || || |||||||| || || ||||||||||| ||| | |||||||| || |||||||||||     | |||||| |  |
ggtagtaaatggtactactatatattttctcataggtcacactgacagctgagtttaatttgttcttacaccactgactgaatatgctgcatatatgcagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCCGCGGCCTGAACGCGGTGACGAACTTCGACATAGCAAGATACGACGTGGA

upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------------------------------------------gtaagttctcagttgtttagagcaatgc----aatgcct--cgctcggtctgatcttg-tttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                                                                                                                              | ||  |   |    ||| |     |||      | |||   | |     ||| || | |||  |  |  ||||||| ||||||||||| || || || |||||||| |||||||| || ||||| || ||||| || ||||| |||||||||||    || ||| |   |  
gtgagtgccggtttcacatgaatttgtaaacattagtggattaccctcgctgcaaatcctggtcgtttctcctgataggacttctgatatcgattccggagacatcagcatattctgggtctcgttgcaatgttgaaaggatttcgcagggtgcccatgttacctaatggttaaaatgaactggctttgtatgactcagGCACACAAGAGGAAGCAGCAGAGGCCTACGACATTGCCGCGATAAAATTCCGTGGAATCAATGCCGTCACAAACTTCGACATGTCTCGTTACAATGCTGC

upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: PP1S66_282V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------------------gtaagttctcagttgtt-taga----gcaatgcaatgcctcgctcggtctgatcttg-tttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                                                                     | |  |   ||||||    |||    |  ||   || |  || ||||  ||   | | | |     |  |||||||||| |||||||| || || ||||||||| | || ||||| || ||||| || |||||||| || || ||||||||||||   || ||||||     
gtgagtggcagtttgacttgggggtttgcagaggaggagggggtttgtatgtgttgttgggatgtggagggagatgtgcagttgcagcagacgtggggatctgatccaacggtcggcgtggcgtgggtgtgtgtgagtcagGCACGCAGGAGGAAGCAGCAGAGGCATACGACCTGGCGGCGATAAAATTCCGTGGAATCAACGCCGTGACAAACTTCGACATCTCTCGGTACGACGCCGG

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: 25 (upstream exon), 32 (downstream exon)
Score: 4

ACACCATCAACAAGGACGCTGGCAAGCCCGGATTGGAAGAGTAGCCGGCAACAAAGATCTTTACCTCGGAACTTTCAgtaagttctc ... aaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtttagagcaatgcaatgcctcgctcggtctgatcttgtttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAA
                              gtctgat  putative branch site (score: 4)
                                      ttgtttaaa  TA-rich tract