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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatatgcgttcgagctgatattctgtcgacttttttcttagagaataactcatcctttattcatattgtgttcccttttttatcaatttttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG

Basic information

species Physcomitrella patens
transcript PP1S9_199V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 7
--aaatatgcgttcgagctgatattctgtcgacttttttcttagagaataactcatcctttattcatattgtgt-tcccttttttatcaatttttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG
   | |    |   |  |  || |  |   |   ||| | ||     | | |   |  |    ||| || || | ||   || ||    ||  ||||   |||||| || || ||    || || || || ||||| ||| | ||||| || || || || || |||||||| || |||||||| ||||||||||||||||||
gctagtccatgaatgctcaaatgtatttaaggtctttatgttgcttgaaatcatctaatcatgtcagatggtttatcatgttgttgatgatcctttt---cagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG

upper sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 7
aaatatgcgttcgagctgatatt--ctgtcgacttttttcttagagaataactcatcctttattcatattgtgttcccttttttatcaatttttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG
 | | |   ||   |   |||||    || |   || |  ||  |    || | ||   || |    | | ||||    ||| | |   || |  |   ||||||||| || ||    || || ||||| || || ||  |||| || ||||| || || || |||||||||||||| |||||||| || ||||||||||||
gactttatttttttgtc-atattagtagtagttcttatgtttttactgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggttt-cagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG

upper sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 7
-----aaatatgcgttcgagctgatattct---gtcgacttttttcttagagaataactcatcctttattcatattgtgttcccttttttatcaatttttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG
        | |   ||   ||    || |     ||  || | || ||    || ||    |||  | || |  |||    |   | | |||  ||  |||    |||||| || || ||    || || ||||||||||| ||| |||| || ||||| ||||| || ||||||||||| || ||||| ||||| ||||||||||||
ttcctctctctctcttaatgcaaccatgcacagatctcctgtgtttttgagaaaaaaactgtccagtgttgactttg----ctactgtctattcatggttt----cagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG

upper sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 7
-aaatatgcgttcgagctgatattctgtcg-acttttttcttagagaataactcatcctttattcatattgtgttccc--ttttttatcaatttttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG
      | | |      | ||    |   | || | |||| |      |    ||    |     ||||||  |||     | | |||  ||  |||    |||||| || || ||    || || ||||||||||| ||  |||| || ||||| ||||| || ||||||||||| || ||||| ||||| ||||||||||||
tggtctttcctctctcttaatgcaataatgcacatatttcctgcgtgtttgagcaaaaatatccaatattgacttcgaaactgtctattcatggttt----cagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG

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|162195435|gb|FC370878.1|FC370878
EST:     GTCAATAAATGGATATTGAAAAATTGTGCAGAGTCGGAGAACATGAACTG                         GATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAA
genomic: GTCAATAAATGGATATTGAAAAATTGTGCAGAGTCGGAGAACATGAACTGgtacgatctg ... ttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAA
EST: gi|162156717|gb|FC333560.1|FC333560
EST:     GTCAATAAATGGATATTGAAAAATTGTGCAGAGTCGGAGAACATGAACTG                         GATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAA
genomic: GTCAATAAATGGATATTGAAAAATTGTGCAGAGTCGGAGAACATGAACTGgtacgatctg ... ttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAA
EST: gi|162179661|gb|FC355719.1|FC355719
EST:     GTCAATAAATGGATATTGAAAAATTGTGCAGAGTCGGAGAACATGAACTG                         GATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAA
genomic: GTCAATAAATGGATATTGAAAAATTGTGCAGAGTCGGAGAACATGAACTGgtacgatctg ... ttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAA

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: 27 (upstream exon), 21 (downstream exon)
Score: 3

TGTCGAGAAGAGGCACACCGGCCCGTGGATTGTGAGACAGTCAATAAATGGATATTGAAAAATTGTGCAGAGTCGGAGAACATGAACTGgtacgatctg ... ttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataactcatcctttattcatattgtgttcccttttttatcaatttttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG
 gaataac  putative branch site (score: 3)
                          ttcccttttttatcaa  putative PPT
                               ttttttatcaattttt  TA-rich tract