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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgaaggggggttgtcgcgcaggctggtagtgttagattttcgagagacgacggatagttgatgtttgttaagctgtttgtggaaattgtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGTATCTGCCTGGATATTTTAAAGGAACAGTGGAGCCCTGCTCTAACTATAT

Basic information

species Physcomitrella patens
transcript PP1S69_142V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S69_142V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA20G05260.1 (Glycine max), 3'ss of exon 1
--acatgaaggggggttgtcgcgcaggctggtagt--gttagattttcgagagacgacggatagt-tgatgtttgttaagctgtttgtggaaattgtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGTATCTGCCTGGATATTTTAAAGGAACAGTGGAGCCCTGCTCTAACTATAT
       || |    || | |    | ||| |  |   ||  |   | |||   |  | |||  | |   || |  | | | | || |  |        || ||||||||||||||||| || || || ||||| || || ||||| || || || || ||||| || || || ||||| |||||||||||||| |||||||| |
atgttctaacgatccttttagtagtgactgttgcttctttgaacactggagctccttcagatgatctcgagtatactcatc-gattataaatgcc----tttcagGTTGCATTCAGGACAAATGTATTTCACCCAAATATAAATAGCAATGGAAGCATTTGCCTTGACATATTGAAGGAGCAGTGGAGCCCTGCGCTAACTATTT

upper sequence: PP1S69_142V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA16G17730.1 (Glycine max), 3'ss of exon 2
acatgaaggggggttgtcgcgcaggctggtagtgttagattttcg-agagacgacggatagttg--atgtttgttaagctgtttgtggaaattgtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGTATCTGCCTGGATATTTTAAAGGAACAGTGGAGCCCTGCTCTAACTATAT
 |   || |        |          | | ||     |  ||  |   |  ||   | || |  ||  ||  || |   ||  |    ||| || |   ||||| ||||| | || |||||||||||||| |||||||| ||||| || ||||||| ||| || ||  | || || || ||||                  
-ctccaacgttaaccaacataagcaactgcattggagtttgctcataataattacaccttgtgggaatagtttgtatggcattctttatcattttgtta--agGTTTCATTCCGCACAAAGGTTTTCCACCCTAACATCAACAGTAATGGAAGTATCTACCTTGACATCCTCAAAGAGCAATGGA------------------
















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|208400830|gb|DC925110.1|DC925110
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|67693812|gb|BJ954045.1|BJ954045
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|67698111|gb|BJ958344.1|BJ958344
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|37852533|gb|BJ610541.1|BJ610541
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|162259705|gb|FC436724.1|FC436724
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|100355061|gb|BY964981.1|BY964981
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTTCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|208392747|gb|DC953644.1|DC953644
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|162272755|gb|FC448771.1|FC448771
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|67698855|gb|BJ959088.1|BJ959088
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|162232470|gb|FC408865.1|FC408865
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|67575390|gb|BJ948214.1|BJ948214
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCANGACCAAAGGTTTTCCACCCGAACATCAATAGTAACGGGAG
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAA-GGTTTTCCACCCGAACATCAATAGTAACGGGAG
EST: gi|67507966|gb|BJ940840.1|BJ940840
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|100352295|gb|BY983136.1|BY983136
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTTCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|208395907|gb|DC911888.1|DC911888
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATANTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|208355817|gb|DC930180.1|DC930180
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|162232471|gb|FC408866.1|FC408866
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|67694209|gb|BJ954442.1|BJ954442
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|208373983|gb|DC944716.1|DC944716
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|100358402|gb|BY983887.1|BY983887
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAAACATCA-TAGTAACGGGAG
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAA-CATCAATAGTAACGGGAG
EST: gi|67570907|gb|BJ943731.1|BJ943731
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGGAG
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGG-AG
EST: gi|18351176|gb|BJ183227.1|BJ183227
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|162259704|gb|FC436723.1|FC436723
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|100403465|gb|BY991213.1|BY991213
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|67569246|gb|BJ942070.1|BJ942070
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|67574694|gb|BJ947518.1|BJ947518
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|208373004|gb|DC940635.1|DC940635
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|67692502|gb|BJ952735.1|BJ952735
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|208384213|gb|DC911307.1|DC911307
EST:     TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
EST: gi|67576952|gb|BJ949776.1|BJ949776
EST:     TTTTCCCCCCGACTATCCATTCAAGCCTCCTAAG                         GTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT
genomic: TTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGT

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: 33 (upstream exon), 29 (downstream exon)
Score: 21

GCAGGCTACGATTATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTATTTCTGGTCACCATTCATTTTCCCCCCGACTATCCATTCAAGCCTCCTAAGgtaggtctgc ... gtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGTATCTGCCTGGATATTTTAAAGGAACAGTGGAGCCCTGCTCTAACTATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagacgacggatagttgatgtttgttaagctgtttgtggaaattgtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGTATCTGCCTGGATATTTTAAAGGAACAGTGGAGCCCTGCTCTAACTATAT
             agttgat  putative branch site (score: 21)
                     tttgttaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatgaaggggggttgtcgcgcaggctggtagtgttagattttcgagagacgacggatagttgatgtttgttaagctgtttgtggaaattgtggttgcagGTTGCATTCAGGACCAAGGTTTTCCACCCGAACATCAATAGTAACGGGAGTATCTGCCTGGATATTTTAAAGGAACAGTGGAGCCCTGCTCTAACTATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG