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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcacatctcctttatttatttagcttttattttcaaactaatcgctccgagctcgcacacaaattctttcagaattttgacttttaaatgctgcagactgctcttgtaacggatcctcatgtgacgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATACCACACTGGACAGCCCTACGAGAAGATAGTCCAAGACACGGACCGAGATT

Basic information

species Physcomitrella patens
transcript PP1S49_191V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_191V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os03g19510.1 (Oryza sativa), 3'ss of exon 8
gtgcacatctcctttatttatttagcttttattttca--aactaatcgctccgagctcgcacacaaattctttcagaattttgacttttaaatgctgcagactgctcttgtaacggatcctcatgtgacgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATACCACACTGGACAGCCCTACGAGAAGATAGTCCAAGACACGGACCGAGATT
                         | ||||||| ||  | | ||| ||    | |||   | |    | | |    ||| | |||| ||    | | ||| |  ||| || || |||  ||   |      |  ||||||| ||||| || |||||||| || ||| |||| || || ||||||||||||||||| ||||||   || |||||   |  ||| || ||||| ||||
-------------------------catttatttccacaagcgaatagc----aactc---cgctggctttct----attgttacttgtatcaccagaagatttttct-gtcactgattttccattatttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATACCACACTGGGCAGCCCCTAGATAAGATCAACGTAGATACTGACCGTGATT
















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|162179727|gb|FC356318.1|FC356318
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|208382931|gb|DC923503.1|DC923503
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGTATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|162179726|gb|FC356317.1|FC356317
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|37851229|gb|BJ609237.1|BJ609237
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|18334691|gb|BJ166708.1|BJ166708
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|7148089|gb|AW510011.1|AW510011
EST:     TCAACCTCGTGG-AGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCA
genomic: TCAACCTC-TGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCA
EST: gi|162159944|gb|FC336197.1|FC336197
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|18341257|gb|BJ173291.1|BJ173291
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|208381909|gb|DC923433.1|DC923433
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|67696515|gb|BJ956748.1|BJ956748
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|208380837|gb|DC923319.1|DC923319
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|37836163|gb|BJ594171.1|BJ594171
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|162268713|gb|FC445210.1|FC445210
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|208372169|gb|DC947972.1|DC947972
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|37851336|gb|BJ609344.1|BJ609344
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
EST: gi|162259738|gb|FC436744.1|FC436744
EST:     ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG                         GCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC
genomic: ATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATAC

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: 24 (upstream exon), 33 (downstream exon)
Score: 10

GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAGgtgcacatct ... acgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATACCACACTGGACAGCCCTACGAGAAGATAGTCCAAGACACGGACCGAGATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttttaaatgctgcagactgctcttgtaacggatcctcatgtgacgactgcagGCTAACGAGATTCTTCATCACAAAGCCAACTTGAACGGTTATCTAGCATACCACACTGGACAGCCCTACGAGAAGATAGTCCAAGACACGGACCGAGATT
                         ttgtaac  putative branch site (score: 10)
     ttaaat  TA-rich tract