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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtctcatgaatctcaatgtgtgaatgaggactcccgcagtgcatgatgttgtctattttagtactcgcattatgacgtgattactttagcaagttcctgaagcgtgtgatgttaaccagagaagttgcaagagcttgaacggtgttgtaactgggttgagtttttgtggcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAAGTTCTG

Basic information

species Physcomitrella patens
transcript PP1S60_85V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 6
gtatgtgtctcatgaatctcaatgtgtgaatgaggactcccgcagtgcatgatgttgtctattttagtactcgcattatgacgtgattactttagcaagttcctgaagcgtgtgatgttaaccagagaagttgcaag---agcttgaacggtgttgtaactgggttgagtttttgtggcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAAGTTCTG
                                                                        | ||  |   || ||| || |    | ||| | |||       |  |    ||  || ||  |||   ||||| |  | || | |||     ||   | ||||||  |||||| ||||| ||||| ||||| || ||| | ||||||||||||||||| |||||||||
------------------------------------------------------------------------gtatagta--gtaatttctgtt-tgaattcattaaggagaaattcatctttagttaaattataagcgcagcttca--gatggtttaatgcaattc--tatttgtgcaacagGTTAATCCTCATACCCATCAGCTAAAATTGTGTGACTTTGGCAGCGCGAAAGTTCTG

upper sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtgtctcatgaatctcaatgtgtgaatgaggactcccgcagtgcatgatgttgtctattttagtactcgcattatgacgtgattactttagcaagttcctgaagcgtgtgatgttaaccagagaagttgcaagagcttgaacggtgttgtaactgggttgagtttttgtggcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAAGTTCTG
                                                                           ||  |||    |||       || | | ||  | |     | ||||     ||  |||  |   |||     ||        |  ||| | || || ||   |||||||| || || |||||||| |||||||||||||| ||||| || || |||||| ||
---------------------------------------------------------------------------tttggacagacttatcaggctaactccatg--gtgacgacttttaaattttgatcttgttat--cttactttgtaagactgatttgttaaattgttatgtt-cagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG

upper sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtgtctcatgaatctcaatgtgtgaatgaggactcccgcagtgcatgatgttgtctattttagtactcgcattatgacgtgattactttagcaagttcctgaagcgtgtgatgttaaccagagaagttgcaagagcttgaacggt--gttgtaactgggttgagtttttgtg-gcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAAGTTCTG
                                                                                                                             || || | |  |  |||  | |||   ||   |||   |    || ||||  | |||||| ||||||||||| || || ||||| || |||||||| |||||||||||||| |||
---------------------------------------------------------------------------------------------------------------------------gtaggaggtccttgtcctttgagggttgatttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGACTTCGGCAGCGCCAAAGTGCTG

upper sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtgtctcatgaatctcaatgtgtgaatgaggactcccgcagtgcatgatgttgtctattttagtactcgcattatgacgtgattactttagcaagttcctgaagcgtgtgatgttaaccagagaagttgcaagagctt-gaacggtgttgtaactgggttgagtttttgtg-gcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAAGTTCTG
                                                                                                                             || || | |  |  ||| | |  |  ||||| ||   |    || ||||  | |||||| ||||||||||| || || ||||| || ||||| ||||||||||||||||| |||
---------------------------------------------------------------------------------------------------------------------------gtaggaggtccttgtccttaggattgatttgta-cttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG

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|162174849|gb|FC351641.1|FC351641
EST:     ATAATGGCATTGGTGTGTGTCACCGAGACATCAAGCCCCAAAACCTGCTG                         GTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAA
genomic: ATAATGGCATTGGTGTGTGTCACCGAGACATCAAGCCCCAAAACCTGCTGgtatgtgtct ... tgtggcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAA




















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: 32 (upstream exon), 34 (downstream exon)
Score: 19

GTACGTAAAGTTGTACACTTATCAGATCTGCCGGTCGATGGCATACATTCATAATGGCATTGGTGTGTGTCACCGAGACATCAAGCCCCAAAACCTGCTGgtatgtgtct ... tgtggcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAAGTTCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagttgcaagagcttgaacggtgttgtaactgggttgagtttttgtggcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAAGTTCTG
                         ttgtaac  putative branch site (score: 19)
                                         tttttgt  putative PPT
                                       agttttt  TA-rich tract