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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcagatcctaacttcgttgtggtacacccatgaggtgcatttaactttatgttttatccgttccttacagtttgcaatagtgtcgtgtgacttaggcttcactttggctgtgcagATGAAAGACTACATTGCTACACCAAAGCCTAATGGTTATCAAAGTTTGCACACCACAGTTATTCCATTCGGCACACAGACTTACTTCCCCATCGAAATTC

Basic information

species Physcomitrella patens
transcript PP1S194_9V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S194_9V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 14
gtgcgcagatcctaacttcgttgtggtacacccatgaggtgcatttaactttatgttttatccgttccttacagtttgcaatagtgtcg-tgtgacttaggcttcactttggctgtgcagATGAAAGACTACATTGCTACACCAAAGCCTAATGGTTATCAAAGTTTGCACACCACAGTTATTCCATTCGGCACACAGACTTACTTCCCCATCGAAATTC
                                            | |  | | || |||     ||| ||| | |||  |    | | | | |  |     ||  |     |||||  || ||||||| |||||||| || |||||||||||||| || |||||| | ||||| ||||| || |||||    |   ||| |   ||||   | ||| |||
-------------------------------------------gtgagttatctgctttccttattcattataatttttacctcttttgattttgccatttctaaaagccagctgtatagGTGAAAGATTACATTGCAACCCCAAAGCCTAATGGATACCAAAGTCTACACACGACAGTGATACCATTTCTGAATGAGAGTATGTTCCATTTGGAAGTTC

upper sequence: PP1S194_9V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
gtgcgcagatcctaacttcgttgtggtacacccatgaggtgcatttaactttatgttttatccgttccttacagtttgcaatagtgtcgtgtgacttaggcttcactttggctgtgcagATGAAAGACTACATTGCTACACCAAAGCCTAATGGTTATCAAAGTTTGCACACCACAGTTATTCCATT-CGGCACACAGACTTACTTCCCCATCGAAATTC
         |    |||| | | ||  ||| || |    || | ||  |||    ||| |   ||  |  |||   ||      | |  |   | | |   || | |||       |||||||||||||| ||||| || ||||| |||||||| ||||||||| | || || || || |||||||| |   |      | |  |||  | | ||| |||
--------gtgtgtactttgctttg-cacatcctt----tgaaatttgcttctaatttaa---gtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGAC-TGGAAGTTC

upper sequence: PP1S194_9V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ30490 (Selaginella moellendorffii), 3'ss of exon 11
gtgcgcagatcctaacttcgttgtggtacacccatgaggtgcatttaactttatgttttatccgttccttacagtttgcaatagtgtcgtgtgacttaggcttcactttggctgtgcagATGAAAGACTACATTGCTACACCAAAGCCTAATGGTTATCAAAGTTTGCACACCACAGTTATTCCATTCGGCACACAGACTTACTTCCCCATCGAAATTC
                                                               ||   ||    |||| ||   || |     |||||   |||        ||  ||||||||||||||||||||||| ||||| || ||||| || |||||| | ||||| | ||| || ||||| ||  || |||| |  |||||  | |||||||
---------------------------------------------------------------gtaagtttttctttgtaa---tgccactgaacttaaaattcg-------tgctcagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC

upper sequence: PP1S194_9V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ23048 (Selaginella moellendorffii), 3'ss of exon 11
gtgcgcagatcctaacttcgttgtggtacacccatgaggtgcatttaactttatgttttatccgttccttacagtttgcaatagtgtcgtgtgacttaggcttcactttggctgtgcagATGAAAGACTACATTGCTACACCAAAGCCTAATGGTTATCAAAGTTTGCACACCACAGTTATTCCATTCGGCACACAGACTTACTTCCCCATCGAAATTC
                                                               ||   ||    |||| ||   || |     |||||   |||        ||  ||||||||||||||||||||||| ||||| || ||||| || |||||| | ||||| | ||| || ||||| ||  || |||| |  |||||  | |||||||
---------------------------------------------------------------gtaagtttttctttgtaa---tgccactgaacttaaaattcg-------tgctcagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCGCTGGAAATTC

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: 9 (upstream exon), 27 (downstream exon)
Score: 1

GTCTGCTATCATGTGTTGGGACTGGTTCATGCTATGTGGCCTCCACTTCCTCAAACGgtgcgcagat ... ggctgtgcagATGAAAGACTACATTGCTACACCAAAGCCTAATGGTTATCAAAGTTTGCACACCACAGTTATTCCATTCGGCACACAGACTTACTTCCCCATCGAAATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttacagtttgcaatagtgtcgtgtgacttaggcttcactttggctgtgcagATGAAAGACTACATTGCTACACCAAAGCCTAATGGTTATCAAAGTTTGCACACCACAGTTATTCCATTCGGCACACAGACTTACTTCCCCATCGAAATTC
 tccttac  putative branch site (score: 1)