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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcgggacgccgtcttggacgtggtggtagtttgtggtggttgtaatcggaccagtgttcctgggccttgaagcaaattcaatgtgtgttggaatttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAGACGCTCGATGGTGCGCTTGACAGCGTCAAATCTAATGGGATTCAGAACA

Basic information

species Physcomitrella patens
transcript PP1S535_3V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S535_3V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDP06255 (Chlamydomonas reinhardtii), 3'ss of exon 2
gtaagtttcgggacgccgtcttggacgtggtggtagtttgtggtggttgtaatcggaccagtgttcctgggccttgaagcaaattcaatgtgtgttggaatttttg---cgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAGACGCTCGATGGTGCGCTTGACAGCGTCAAATCTAATGGGATTCAGAACA
                |||   | ||   |   |  |    | |   |     |  ||   |   |    | ||         | |  |   | ||    |   ||      |||| ||||| || ||||||||||| || |||||||||||||||| || ||||| ||| ||  | || ||  ||                            
-------------tcacgtaccgtaccctgcc-tgctccccgctacctcccccctcactgattacctcctgtctccccctccctcccctccctcttctcctccctgtcttatagATCTGTGTGGAGACCATGATGCACCTCACCTGCACCAACATGCCGGAGGAGAAGCTGGAGAGCGCTCTGCACGAG-------------------------
















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|100448106|gb|CJ972405.1|CJ972405
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|100383525|gb|BY950309.1|BY950309
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18350683|gb|BJ182734.1|BJ182734
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|100416531|gb|BY975434.1|BY975434
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18375220|gb|BJ206798.1|BJ206798
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|100363821|gb|BY966187.1|BY966187
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18352910|gb|BJ184965.1|BJ184965
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18347625|gb|BJ179672.1|BJ179672
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18366669|gb|BJ198748.1|BJ198748
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18328689|gb|BJ160694.1|BJ160694
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|67709514|gb|BJ965330.1|BJ965330
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCGTCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18349080|gb|BJ181129.1|BJ181129
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18366288|gb|BJ198367.1|BJ198367
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18371978|gb|BJ203580.1|BJ203580
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|100435526|gb|BY960956.1|BY960956
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|100418865|gb|BY975777.1|BY975777
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18352436|gb|BJ184490.1|BJ184490
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|67718564|gb|BJ968823.1|BJ968823
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18354016|gb|BJ186071.1|BJ186071
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|100452988|gb|CJ975544.1|CJ975544
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18329100|gb|BJ161106.1|BJ161106
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|162181090|gb|FC357574.1|FC357574
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|162233053|gb|FC408460.1|FC408460
EST:     CGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: CGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|100378609|gb|BY968688.1|BY968688
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|100371077|gb|BY985927.1|BY985927
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18360297|gb|BJ192359.1|BJ192359
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18371953|gb|BJ203555.1|BJ203555
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACANGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|162164651|gb|FC340698.1|FC340698
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|67704345|gb|BJ964578.1|BJ964578
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTT
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTT
EST: gi|67572507|gb|BJ945331.1|BJ945331
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18354995|gb|BJ187054.1|BJ187054
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|100427543|gb|BY977550.1|BY977550
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18329699|gb|BJ161705.1|BJ161705
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18357118|gb|BJ189177.1|BJ189177
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
EST: gi|18342724|gb|BJ174759.1|BJ174759
EST:     GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATG                         ATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG
genomic: GGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAG

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: 30 (upstream exon), 33 (downstream exon)
Score: 7

CATGGTCATGCACCAGCCTGCGTTTTGTGACATCACCTGGGGAGCTGGAGGGTCGACCTCCGCTGTCACCCTCGACATTGCCAACAAGATGCAGAACATGgtaagtttcg ... ttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAGACGCTCGATGGTGCGCTTGACAGCGTCAAATCTAATGGGATTCAGAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accagtgttcctgggccttgaagcaaattcaatgtgtgttggaatttttgcgcagATTTGTGTCGAAACCATGATGCATCTTACCTGCACCAACATGCTGGTGGAGACGCTCGATGGTGCGCTTGACAGCGTCAAATCTAATGGGATTCAGAACA
                                            tttttgc  CT-rich tract
                        aaattcaat  TA-rich tract