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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatctttctcataatgtcctccttcgtcttggagtagatgctgtttcacacatgccattggtagagttgtgactgaattgtgtgatggggtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG

Basic information

species Physcomitrella patens
transcript PP1S65_6V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
-----gtgagaatctttctcataatgtc--ctccttcgtcttggagtagatgctgtttcacacatgccattggtagagttgtgactgaattgtgtgatggggtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
      ||||     |||   || |      || ||||| |||||  ||    ||||      | || |   | |  |  |   || |  | | |   |       | |||| ||||||||||||| || |||||||||||||| || ||||| ||||| |||||||| ||||| |||
gtaagatgagcgcgcttcatgtattcctggttctttcgttttgga-caggaattgtt--gttgaagcta--aggaaggcagcatctcacat-tatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG

upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G129209_T01 (Zea mays), 3'ss of exon 1
gtgagaatctttctcataatgtcctccttcgtcttggagtagatgctgtttcacacatgccat-tggtagagttgtg-actgaattgtgtgatggggtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
                            |  |    ||||   |    |       |||| ||   ||  || | |  |    ||||| || |       ||||||||||||||||||||| || |||||||||||||| || || ||||| || |||||||| |||||||| 
---------------------------gtaattagcgagtcagttaaatgcaggcaatgcaatgcagtgcagctctatatattattgtatgtt----caagtgcagGCGGATTAGCCACAGGACGCACCACCAGAACCACGGCCACGTGGACAAGGACGAGTCATGGCATCCC

upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G06950.1 (Glycine max), 3'ss of exon 2
gtgagaatctttctcataa-tgtcctccttcgtcttggagt-agatgctgtttcacacatgcca--------ttggtagagtt--gtgactgaattgt--------gtgatggggtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
|   |  || || |   || | | |   |||   |||   | | ||  | ||| |    ||  |        |||||    ||     ||  ||   |         | ||||  |   |||||| | ||||||||||| |||||||| ||||||||||| ||||| ||||| || || || |||  ||| 
ggtcggttccttttagcaacttttcatgttcactttgtccttaaatttttttttatgtttgttaaaaaatctttggtctgatttaacaacctaaccatttttacaactcatggattttttgcaGGAGAATTAGCCACAGGACTCACCATCAGAACCATGGCCATGTTGAGAAGGATGAATCATGGGTTCC-

upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G27190.1 (Glycine max), 3'ss of exon 2
gtgagaatctttctcataatgtcctc-------cttcgtcttggagtagatgctgtt-tcacacatgccattggta-gagttgt-gactgaattgtgtgatggg--gtgggt-------gcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
  |   ||   | | || |  |  ||       ||| ||| |  | ||  |  | || | | | |  |  |||||  || ||||  ||   |   | | |       ||| |       ||||| | ||||||||||| |||||||| ||||||||||| ||||| ||||| || || || |||  ||||
--gtcgattccttttatcaacttttcatgttcactttgtccttaaatatttttttttgttaaaaaatcttttggtctgatttgtcaacctcaccattttactactcatggatatcttttgcagGAGAATTAGCCACAGGACTCACCATCAGAACCATGGCCATGTTGAGAAGGATGAATCATGGGTTCCG

upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G39230.1 (Glycine max), 3'ss of exon 2
--gtgagaatctttctcataatgtcctc-cttcgtcttggagtagatgctgtttcacacatgccattggtagagttgtgactgaattg--tgtgatggggtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
  || ||  |||   | |   ||      |  | | ||||| | |   |       || ||   ||| |   | |    ||  |||||  | ||||||  |   |||||| | |||||||||||||||||||| || |||||||| ||  | ||||| || ||||| |||  ||| 
ctgttagcttctgagtaaacgtggaaaaaccacattttggatttggaac-------caaattttatttgataaatgacaaccaaattgattttgatggattt--tgcagGAGAATTAGCCACAGAACTCACCATCAAAACCATGGACACATTGAGAAGGATGAGTCATGGGTTCCA

upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagaatctttctcataatgtcctccttcgtcttggagtagatgctgtttcacacatg--ccattggtagagttgtgactgaat-tgtgtgatggggtggg---------tgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
  | || | || ||   |||  | ||  |    |   |     | || | |     |||   || | | ||| |  |  |  | | |   |||     |  |         || ||| |||||||||||||||||||||||||||||||||| ||||| ||||| ||||| || |||||||| 
--gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcacttgaagaataatatcacattcttcatgacaatatttgaattttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT

upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G11170.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagaatctttctcataatgtcctccttcgtcttggagt-agatgctgtttcacacatgccattggtagagttgtgactgaattgtgtgatggggtggg--tgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
                           |  || |||   | |||   |  ||| |  |  ||| | | ||| |     ||   |  ||| |     ||    |||||| | ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| || |||||||| 
--------------------------gtgagttttgctttcagaccattcttctctaaaaccacttgcagaatctcatcttcttcatgtaaaaatatgactttgcagGAGAATTAGTCACAGAACTCACCACCAGAACCATGGACATGTTGAGAATGACGAATCTTGGCATCCT

upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgagaatctttctcataatgtcctccttcgtcttggagtagatgctgtttcacacatgccattggtagagttgtgactgaattgt-gtgatggggtgggt---gcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
       |   | | | | |||     |  | |  | |   ||   | | | ||| |||  |||  ||   |    | |||| |||    ||    |||||   ||||| | || |||||| | || ||||||||||||||||| ||||| || ||||||||||| |||  ||||
-------taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgt-atttataatttacgaattgaaatgttaatattaattgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG

upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ23113 (Selaginella moellendorffii), 3'ss of exon 2
gtgagaatctttctcataatgtcctccttcgtcttggagtagatgctgtttcacacatgccattggtagagttgtgactgaattgtgtgatggggtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
                                      |||  |    |||  ||  |    ||  | |  | | |  | || | ||||          | |||| |||| |||||| | || || |||||||| || || ||||| |||||||||||||| |||||||| 
--------------------------------------gtacgtatgcttttccatttcttgtt--tggcttagagcttaaactttgtgg------aaatccagGAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCA

upper sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20170 (Selaginella moellendorffii), 3'ss of exon 2
gtgagaatctttctcataatgtcctccttcgtcttggagtagatgctgtttcacacatgccattggtagagttgtgactgaattgtgtgatggggtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG
                                      |||  |    |||  ||  |    ||  | |  | | |  | || | ||||          | |||| |||| |||||| | || || |||||||| || || ||||| |||||||||||||| |||||||| 
--------------------------------------gtacgtatgcttttccatttcttgtt--tggcttagagtttaaactttgtgg------aaatccagGAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCA

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|162180305|gb|FC355310.1|FC355310
EST:     TTGATCGGTCACCTAACTCACTCATCCATACTTGTTCCATACCACGGGTG                         GCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGA
genomic: TTGATCGGTCACCTAACTCACTCATCCATACTTGTTCCATACCACGGGTGgtgagaatct ... gtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGA
EST: gi|162184125|gb|FC358871.1|FC358871
EST:     TTGATCGGTCACCTAACTCACTCATCCATACTTGTTCCATACCACGGGTG                         GCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGA
genomic: TTGATCGGTCACCTAACTCACTCATCCATACTTGTTCCATACCACGGGTGgtgagaatct ... gtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGA
EST: gi|162225848|gb|FC402140.1|FC402140
EST:     TTGATCGGTCACCTAACTCACTCATCCATACTTGTTCCATACCACGGGTG                         GCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGA
genomic: TTGATCGGTCACCTAACTCACTCATCCATACTTGTTCCATACCACGGGTGgtgagaatct ... gtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGA
EST: gi|162238964|gb|FC417715.1|FC417715
EST:     TTGATCGGTCACCTAACTCACTCATCCATACTTGTTCCATACCACGGGTG                         GCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGA
genomic: TTGATCGGTCACCTAACTCACTCATCCATACTTGTTCCATACCACGGGTGgtgagaatct ... gtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGA

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: 21 (upstream exon), 35 (downstream exon)
Score: 10

TGGTCATGGCAGCTTTTCCAACAACAAGACGCTGAACAGTTTGATCGGTCACCTAACTCACTCATCCATACTTGTTCCATACCACGGGTGgtgagaatct ... gtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaatctttctcataatgtcctccttcgtcttggagtagatgctgtttcacacatgccattggtagagttgtgactgaattgtgtgatggggtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA