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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttctatcactaatatcacaagcacattggctctttgcctgacttaataatatattggaaagtttcgttgcatcaatgaattgctaaaggatat...

Basic information

species Physcomitrella patens
transcript PP1S181_117V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S181_117V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AC198982.3_FGT006 (Zea mays), 5'ss of exon 3
CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgt------ctgtcttctat-cactaatatc---acaagcacattggctctttgcctgacttaataatatattggaaagtttcgttgcatcaatgaattgct-aaaggatat-------
|||||||| || ||| ||||||| || |||||  | ||||| |||||||||||||||||||| || || ||||| || ||||||||  | |||||       |||  |  ||    |  ||||   |||||||   |       |   |  |||    ||  |||| |    ||| ||     ||    ||||| |||   | |       
CAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTTGTTCATTTGCAGgtaaagttttgtgatggatatgtttttatctaaacaagcatggttctgaaatctgttgcttgtacattcattgtatttcttcctttgtgaaactccttgcttaaaatttgttctgcag

upper sequence: PP1S181_117V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G047695_T01 (Zea mays), 5'ss of exon 5
CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtc-tgtcttctatcactaatat-cacaagcacat-tggctctttg--cctgacttaataatatattggaaagtttcgttgcatcaatgaattgctaaaggatat
|||||||| || ||| ||||||| || |||||  | ||||| |||||||||||||||||||| || || ||||| || || |||||  | |||||   ||  | |      | |||    || ||  | ||| |||     | |   |   ||| | |      || || || |||||  |    |       |    
CAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAGgtaacgtgctgtgatggaattatgtttaaacaagtatggttctgaaatcttttttccctaaaaaacgcaggagatttgt-gcatccttaggctatctccag----
















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|162162595|gb|FC338689.1|FC338689
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162221408|gb|FC397217.1|FC397217
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162258112|gb|FC433894.1|FC433894
EST:     AGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: AGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162233878|gb|FC409728.1|FC409728
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162198877|gb|FC372904.1|FC372904
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162162497|gb|FC339215.1|FC339215
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162152120|gb|FC328710.1|FC328710
EST:     TATTCAAGCAAGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTC
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTC
EST: gi|162158626|gb|FC335526.1|FC335526
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT

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: 35 (upstream exon), 35 (downstream exon)
Score: 10

CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTTTTGGCCTATAAGAGTAACTGCAAAGCGATGTTGAAGGCGGTTGATGACA




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