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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCCTTGGTAAGCAGGTCCCAGCAACATGGCGGACAAGGCGTGCACCGTGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcgctggccctcctctccgttctttctcccatcggtttcccaactactcggttggattgagcttttctgggattgagctcttgttggttctgt...

Basic information

species Physcomitrella patens
transcript PP1S37_112V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_112V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT3G04920.1 (Arabidopsis thaliana), 5'ss of exon 1
ATTGCCTTGGTAAGCAGGTCCCAGCAACA-TGGCGGACAAGGCGTGCACCGTGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcgctggccctcctctccgttctttct-cccatcggtttcccaactactcggttggattgagcttttctggga-ttgagctcttgttggttctgt----
 |  | ||  |      |    ||||| | |||| || ||||||  |||| | || ||  | |||||||||||||||||||| ||| |||| ||||||||||| ||   |  |     |  ||||   ||| ||| |  |||  |||      |  ||   ||| ||  | |||  ||||| |  || | |  || | | ||     
-TCACTTTAATCCTTGAGAAGTAGCAAAAATGGCTGAAAAGGCGGTCACCATCCGAACCAGGAAATTCATGACCAACAGACTTCTCTCCAGGAAGCAGTTCgtgagttccattattttttttctcttctctatctgcatatcatttt------tgttcttctgggttttgttttaatgggaatctagttataatttgatatgaaccc

upper sequence: PP1S37_112V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 1
-ATTG-CCTTGGTAAGCAGGTCCCAGCAACATGGCGGACAAGGCGTGCACCGTGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcgctggccctcctctccgttctttctcccatcggtttcccaactactcggt-tggattgagcttttctgggattgagctcttgttggttctgt-
 | ||  || || ||| |  || ||||  ||||||||| || ||   |||  |  | ||  | || |||||||||||||| || |||||||||||||| ||||| ||     |   | ||    ||| || |     |   | || |  |  || | | || | || |||      ||    || || |        |  | | 
GACTGATCTCGGAAAGTAAATCGCAGC--CATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagt--tcccatctctatgttccattttgcaatctcacagtgttacgtcttcgctgtatcgaatgataaaaactatagtttaggtagaaacaatcttata

upper sequence: PP1S37_112V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EDP07861 (Chlamydomonas reinhardtii), 5'ss of exon 1
ATTGCCTTGGTAAGCAGGTCCCAGCAACATGGCGGACAAGGCGTGCACCGTGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcgctggccctcctctccgttctttctcccatcggtttcccaactactcggttggattgagcttttctgggattgagctcttgttggttctgt
                     | |||| ||| |||||||| |||||||  | ||||||||||| |||||||||||| | |||||     |   ||| ||||| ||      ||||           | ||  ||  |  ||   ||   |   || |       ||| || |  |   |||| ||               
---------------------CGGCAAGATGTCGGACAAGACGTGCACTATCCGCACTCGCAAGTTCATGACCAACCGGCTGCTGCAGCGCCGGCAATTCgtgagt----ttggcatggagaaggctgctggctggccgcgcgctctggaggcctggac---gctga-ctctcatcatattgcgcag-------------

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|18368342|gb|BJ200427.1|BJ200427
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|37849875|gb|BJ607883.1|BJ607883
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67709358|gb|BJ965174.1|BJ965174
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67718399|gb|BJ968658.1|BJ968658
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|18344985|gb|BJ177026.1|BJ177026
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|162249820|gb|FC427597.1|FC427597
EST:     TGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67709437|gb|BJ965253.1|BJ965253
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67703265|gb|BJ963498.1|BJ963498
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67727511|gb|BJ977770.1|BJ977770
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67703950|gb|BJ964183.1|BJ964183
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67691760|gb|BJ951993.1|BJ951993
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|162211671|gb|FC387959.1|FC387959
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|162249821|gb|FC427598.1|FC427598
EST:     TGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67728039|gb|BJ978298.1|BJ978298
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|162202366|gb|FC379179.1|FC379179
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|162269513|gb|FC445069.1|FC445069
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|208345424|gb|DC912999.1|DC912999
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67719775|gb|BJ970034.1|BJ970034
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|162269512|gb|FC445068.1|FC445068
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67719209|gb|BJ969468.1|BJ969468
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|18346009|gb|BJ178052.1|BJ178052
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|37825126|gb|BJ583192.1|BJ583192
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67724705|gb|BJ974964.1|BJ974964
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|18361756|gb|BJ193823.1|BJ193823
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67716187|gb|BJ966447.1|BJ966447
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|37824188|gb|BJ582254.1|BJ582254
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|67574155|gb|BJ946979.1|BJ946979
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
EST: gi|208355156|gb|DC926765.1|DC926765
EST:     TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTC                         ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG
genomic: TGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG

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: 103

ATTGCCTTGGTAAGCAGGTCCCAGCAACATGGCGGACAAGGCGTGCACCGTGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcg ... gtttgtgcagATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG




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