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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgaaaaaaactagaatagttggtcgcattttcatcttagaaatgactcgcaattctatcctgcccatcaattgatcgttgtttctgtgcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTCCAGGAAAGGGCAACATTCATTTCACATGGTAACACTGCTCGGCACGCCA

Basic information

species Physcomitrella patens
transcript PP1S146_17V6.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S146_17V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os04g31070.1 (Oryza sativa), 3'ss of exon 2
taatgaaaaaaact-agaatagttggtcgcattttcatcttagaaatgactcgcaattctatcc-tgcccatcaattgatcgttgtttctgtgcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTCCAGGAAAGGGCAACATTCATTTCACATGGTAACACTGCTCGGCACGCCA
 | | |    |  | |||||     || | ||  | || | | |||| | |  || |  || ||  |    | | || | |  |  | |    |   ||||||| ||   ||| ||||| |||||||||||||||||| ||||||| || || || ||||| || ||||| || || ||||| || |||||  |||||||||
-attcactgcattttagaatcaaccgtggtatggttat-tcataaattaatttcattgttagccacgaatctaatttcacctcttgtacctaccttctgcagGATCCAGGAACTGAGAATAATCCCTACTTGGGTTTCCTTTACACATCATTTCAAGAAAGAGCTACATTTATATCCCATGGCAATACTGCAAGGCACGCCA

upper sequence: PP1S146_17V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AC215690.3_FGT002 (Zea mays), 3'ss of exon 2
taatgaaaaaaactagaatagttg-gtcgcattt-tcatcttagaaatgactcgcaattctatcctgcccatcaattg-atcgttgtttctgtgcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTCCAGGAAAGGGCAACATTCATTTCACATGGTAACACTGCTCGGCACGCCA
  || ||   |   | |||| |   ||||  |     ||  | | ||    | | ||      | |     | | ||| ||  |  ||||| |   || |||||| |||  ||| |||||||| ||||||||||||||| | ||||| || ||||| ||||||||||||||  | || ||||| || |||||  |||| ||||
-gataaatggagagaaaataatgatgtcgagtgagctattctggtaactcgttg-aacatagccataagtgtaatttgtattatcatttctttcttat-gcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA

upper sequence: PP1S146_17V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G026793_T01 (Zea mays), 3'ss of exon 2
-taatgaaaaaaactagaatagttggt----cgcattttcatcttagaaatgactcgcaattctatcctgcccatcaattgatcgttgtttctgtgcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTCCAGGAAAGGGCAACATTCATTTCACATGGTAACACTGCTCGGCACGCCA
  |||   | ||||  | | | ||  |     | | |    | ||    || ||| | | |  ||        ||  ||  ||  |  ||||| |   || |||||| |||   || |||||||| || |||||||||||| ||||||| || || || ||||| ||||||||  | |||||||| ||||||||  | || ||||
agaattggagaaacggggaaaattaatgatgtggagtgagctgttttggataacttgtagtcataagtg--taatttat--attttcatttctttcttat-gcagGATCCTGGGACTGAGAACAACCCGTACTTGGGTTTCCTTTACACATCATTTCAAGAAAGAGCAACATTTGTATCACATGGAAACACTGCAAGACATGCCA

upper sequence: PP1S146_17V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM5G852502_T01 (Zea mays), 3'ss of exon 2
-taatgaaaaaaactagaatagttggtcgcattttcatcttagaaatgactcgcaattctatcctgcccatcaattgatcgttgttt-ctgtg-cgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTCCAGGAAAGGGCAACATTCATTTCACATGGTAACACTGCTCGGCACGCCA
 |  |      |  | |  |  ||  ||   |||  || |  |  |   ||   || | | |        | |  ||  | || ||| ||||| |  || ||||| |||   || ||||| ||||| ||  | |||||| | |||||||||||||| ||  |||| || ||||| ||||| || ||||||||||| |||||||
atcttttgttcacttcgtttttttcttc---tttaaatataggctacttcttataaatatgtaggaggactaatatgtactttctttactgtgtccttttcagGATCCTAGGACTGAGAATAATCCTTATCTTGGTTTCATCTACACCTCCTTCCAAGAGCGGGCGACCTTCATCTCACACGGGAACACTGCTCGTCACGCCA

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|162256526|gb|FC432836.1|FC432836
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTCCCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162187541|gb|FC363803.1|FC363803
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162211398|gb|FC387836.1|FC387836
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|37853571|gb|BJ611579.1|BJ611579
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|100364909|gb|BY947969.1|BY947969
EST:     ACATGANNAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAAACA-TCCCTACTTTGGGGTTCGTT-ACAC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAA-CAATCCCTACTT-GGGTTTCGTTTACAC
EST: gi|18335114|gb|BJ167132.1|BJ167132
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162181622|gb|FC357924.1|FC357924
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162181623|gb|FC357925.1|FC357925
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTTGGGTT-CGTTTACACCTCCTT
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTT-GGGTTTCGTTTACACCTCCTT
EST: gi|208372239|gb|DC948042.1|DC948042
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162256527|gb|FC432837.1|FC432837
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCCTT
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCC-TT
EST: gi|18364750|gb|BJ196823.1|BJ196823
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|37852046|gb|BJ610054.1|BJ610054
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|18338592|gb|BJ170616.1|BJ170616
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162196308|gb|FC373532.1|FC373532
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|18332608|gb|BJ164621.1|BJ164621
EST:     AGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGANCAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: AGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162270939|gb|FC447358.1|FC447358
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|67699825|gb|BJ960058.1|BJ960058
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162188014|gb|FC365004.1|FC365004
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162216942|gb|FC391942.1|FC391942
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|18361135|gb|BJ193200.1|BJ193200
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|162187542|gb|FC363804.1|FC363804
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|18333722|gb|BJ165737.1|BJ165737
EST:     TGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: TGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
EST: gi|100419057|gb|BY975836.1|BY975836
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTAC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTAC
EST: gi|100411895|gb|BY992393.1|BY992393
EST:     CATGAAAAGCATTGAGAAA-CTATCCAGTAACCTTAT-GGATCTGGCATG                         GACCCTCAAACAGA
genomic: CATGAAAAGCATTGAGAAAACTATCCAGTA-CCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGA
EST: gi|162220398|gb|FC395753.1|FC395753
EST:     ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATG                         GACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC
genomic: ACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTC

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: 29

TCGCCACGGAGATCTTTTAAATAAATATTTATACTTGACTGGCCGGGTGGACATGAAAAGCATTGAGAAAACTATCCAGTACCTTATTGGATCTGGCATGgtgagcgttt ... gcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTCCAGGAAAGGGCAACATTCATTTCACATGGTAACACTGCTCGGCACGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactcgcaattctatcctgcccatcaattgatcgttgtttctgtgcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTCCAGGAAAGGGCAACATTCATTTCACATGGTAACACTGCTCGGCACGCCA
                          aattgat  putative branch site (score: 29)
        aattctat  TA-rich tract