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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatttcaagtaacttcctcaatttttaatgttcaatgttgataattaactctgtgacaatggggagtttggatttgacaagtcgttgattcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG

Basic information

species Physcomitrella patens
transcript PP1S85_75V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 12
tttatttcaagtaacttcctcaatttttaatgttcaatgttgataattaactctgtgacaatggggagtttggatttgacaagtcgttgattcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG
                     |  | |||    || ||     |  ||   || |  |  ||| | |   || ||| ||||  |  |   |||  | ||| | || || || |||||||| || |||||||| || |||||||||||||| || |||||||| ||  | || || || ||||||
-------------------gtacctattatgagtccataggctttgtt--ttcagacatgatgtgtaagatgaatt-gacatctactgttttctgttcagCTTTATGCCAACTATGCTATTGGAAAGGATGTTCAGGCCATGAAGGCTGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 13
tttatttcaagtaacttcctcaatttttaatgttcaatgttgataattaactctgtga-caatggggagtttggatttga--caagtcgtt--gattcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG
               |  || |  || |  ||||||      ||| |||  | | ||  ||      ||  |  || | |  || ||  ||   |||  || ||| | |||||||||||||||||||| ||||||||||| || ||||| || ||||| ||||| |||||  | || || || || |||
--------------gtctctgatcttgttttgttcatcac--atagttatttttctgttcatcacatagactatatctcattcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
-tttatttcaagtaacttcctcaatttttaatgttcaatgttgataattaactctgtgacaatggggagtttggatttgacaagtcgttgattcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG
 ||   | |   |||       ||  ||   ||   || || | | |     ||    | | |   || ||   | |||||||     |  ||   | ||| | |||||||||||||| ||||| || ||||| ||||||||||| ||||| || ||||| |||||  ||||||| || ||||||
gttctctacctataaag-----aaccttacttgcctaaagtagctcacatgttcat--atagtatcgaatt---aattgacaacattctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 13
tttatttcaagtaacttcctcaatttttaatgttcaatgttgataattaactctgtgacaatggggagtttggatttgacaagtcgttgattcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG
                     | | ||| ||||||   | ||    || ||  | |  |  || | |  |   |  | |   |    |  ||| || ||| | || ||||||||||| || ||||||||||| ||||| ||||| |||||||| ||||| |||||  | ||||| || ||||||
-------------------gtagtatttgatgttcgg-gctgc--gttcaccttct--ctttgagcacgtcccaactaatgcgattcttcttcttt-cagCTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
tttatttcaagtaacttcctcaatttttaatgttcaatgttgataatta--actctgtgacaatggggagtttggatttgacaagtcgttgattcat-tgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG
          ||||  | |  ||   |||| ||    | || ||  |    | | | |  |  |  ||  |    |     |  || | |  ||||  | ||| | || || ||||||||||| || |||||||| || || ||||| |||||||| |||||||||||  | ||||| || ||||||
----------gtaagattcagaaggcttaa-gtgtgtttttaattttctccattatattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG

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|37827904|gb|BJ585916.1|BJ585916
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|208370179|gb|DC944404.1|DC944404
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|37844176|gb|BJ602184.1|BJ602184
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|162274940|gb|FC450591.1|FC450591
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|162274941|gb|FC450592.1|FC450592
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|208345114|gb|DC925440.1|DC925440
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|37848050|gb|BJ606058.1|BJ606058
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|67698442|gb|BJ958675.1|BJ958675
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|162190699|gb|FC367585.1|FC367585
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|37833609|gb|BJ591621.1|BJ591621
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
EST: gi|18337987|gb|BJ170011.1|BJ170011
EST:     CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAG                         TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG
genomic: CTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTG

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: 32 (upstream exon), 35 (downstream exon)
Score: 17

AGTGCTATAGGACAGGGGATGACTCGAAAGGATCATTCCGAAGTTTCCAATCAGgttcatacta ... ttcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaactctgtgacaatggggagtttggatttgacaagtcgttgattcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG
                                            attcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatttcaagtaacttcctcaatttttaatgttcaatgttgataattaactctgtgacaatggggagtttggatttgacaagtcgttgattcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA