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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtggtttgcctggtgcacgagcatgcgtgggggctgcgggggaagtttgacctggggagggaacgcgagcgccggggtgggattggattgcgtaatgggggaagcagaggcgagtgatgaggacgcttggtgaacaagcatgctgacgctgaggtttgtgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCAGCGTTGGTCGCAGCGGACGTGGGGATGGCGATAGGAGCGGGGACGGACA

Basic information

species Physcomitrella patens
transcript PP1S83_69V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_69V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G144083_T01 (Zea mays), 3'ss of exon 5
gttcgtggtttgcctggtgcacgagcatgcgtgggggctgcgggggaagtttgacctggggagggaacgcgagcgccggggtgggattggattgcgtaatgggggaagcagaggcgagtgatgaggacgcttggtgaacaagcatgctgacgctgaggtttgtgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCAGCGTTGGTCGCAGCGGACGTGGGGATGGCGATAGGAGCGGGGACGGACA
                                         | | |   | |  || | |    |    |       |   | |  |   |  |||   |||     |     |  | | |  || ||| | | |   |  |  | ||||| |  |    |||     ||||  | | || | | | ||||| ||||| || ||||| |||||||| || || ||| | ||| | || ||||||||| |||||||||| |||||||||||| 
-----------------------------------------gtgaggtatctatccggtgtttcgtttcc---ttttgtactcgtttccaagagcgctctggactctggtccagttaattactagtacg-tagcttctcctgagtcctgacacaaa---ctgt----cgcagCTGTCTGGAAGGACCGTGGCGATGGTTGGCGACGGGATCAACGACTCCCCCGCGCTCGTCTCGGCCGACGTGGGGCTGGCGATAGGCGCGGGGACGGACG

upper sequence: PP1S83_69V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ17461 (Selaginella moellendorffii), 3'ss of exon 5
gttcgtggtttgcctggtgcacgagcatgcgtgggggctgcgggggaagtttgacctggggagggaacgcgagcgccggggtgggattggattgcgtaatgggggaagcagaggcgagtgatgaggacgcttggtgaacaagcatgctgacgctgaggtttgtgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCAGCGTTGGTCGCAGCGGACGTGGGGATGGCGATAGGAGCGGGGACGGACA
                                                                                                                    |||  |  |     |||| |||||| |   |||   ||     |||   | | |||||| |||||| | | || || |||||||| || || ||||||||||| || ||| |||| || ||||||||||| |||||||| ||||| ||||| ||||
---------------------------------------------------------------------------------------------------------------gtaaaagttctttgcgtttttggagaacaaact--ctggatct----cttgctcgttccagGCGACAGGGATGGCAGTAGCGATGGTGGGCGATGGTATCAACGATTCCCCGGCGCTGGTGGCCGCGGACGTGGGCATGGCGATTGGAGCCGGGACCGACA

upper sequence: PP1S83_69V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ28784 (Selaginella moellendorffii), 3'ss of exon 5
gttcgtggtttgcctggtgcacgagcatgcgtgggggctgcgggggaagtttgacctggggagggaacgcgagcgccggggtgggattggattgcgtaatgggggaagcagaggcgagtgatgaggacgcttggtgaacaagcatgctgacgctgaggtttgtgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCAGCGTTGGTCGCAGCGGACGTGGGGATGGCGATAGGAGCGGGGACGGACA
                                                                                                                    |||  |  | |   |||| ||| || |   |||   ||     |||   | | |||||| |||||| | | || || |||||||| || || ||||||||||| || ||| |||| || ||||||||||| |||||||| ||||| ||||| ||||
---------------------------------------------------------------------------------------------------------------gtaaaagttctttgcatttttggagaagaaact--ctggatct----cttgctcgttccagGCGACAGGGATGGCAGTAGCGATGGTGGGCGATGGTATCAACGATTCCCCGGCGCTGGTGGCCGCGGACGTGGGCATGGCGATTGGAGCCGGGACCGACA

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|162275157|gb|FC451744.1|FC451744
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162152469|gb|FC328032.1|FC328032
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162180046|gb|FC355896.1|FC355896
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162267246|gb|FC442658.1|FC442658
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162154573|gb|FC330783.1|FC330783
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162266238|gb|FC442170.1|FC442170
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162192499|gb|FC369129.1|FC369129
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162198739|gb|FC374222.1|FC374222
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162205789|gb|FC381027.1|FC381027
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162263866|gb|FC439174.1|FC439174
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162263638|gb|FC440122.1|FC440122
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|67572499|gb|BJ945323.1|BJ945323
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162235274|gb|FC412241.1|FC412241
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162208862|gb|FC384998.1|FC384998
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162151846|gb|FC328092.1|FC328092
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162276530|gb|FC452910.1|FC452910
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162205788|gb|FC381026.1|FC381026
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162188683|gb|FC364593.1|FC364593
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|22132295|gb|BQ827083.1|BQ827083
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162173031|gb|FC348656.1|FC348656
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162180399|gb|FC355820.1|FC355820
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162264369|gb|FC440535.1|FC440535
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162189736|gb|FC366790.1|FC366790
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162218370|gb|FC394752.1|FC394752
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|22131683|gb|BQ826742.1|BQ826742
EST:     GAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: GAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162246406|gb|FC419942.1|FC419942
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162153131|gb|FC329537.1|FC329537
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162275156|gb|FC451743.1|FC451743
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162273416|gb|FC449865.1|FC449865
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162276531|gb|FC452911.1|FC452911
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA

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: 200

CACAGCCGTGGCGATTGCGAGGGAGTTGGGAATCGAGAGGCCATGCGTGCACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCAGCGTTGGTCGCAGCGGACGTGGGGATGGCGATAGGAGCGGGGACGGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgaggacgcttggtgaacaagcatgctgacgctgaggtttgtgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCAGCGTTGGTCGCAGCGGACGTGGGGATGGCGATAGGAGCGGGGACGGACA
                           tgctgac  putative branch site (score: 200)