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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA

Basic information

species Physcomitrella patens
transcript PP1S37_304V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                                                                               | | || |   ||  | |   |  |  ||   ||  || |         |   ||||  ||  |||    ||| |   |     |||    |  |    ||||||||||||| |||||||| || |||||||| ||   ||||||||| ||||| || || ||||||||||| ||| | ||||||||| |||||||||||||
-------------------------------------------------------------------------------gatattatcatcatggcttttatggggttatttgaaaaatctg-acatctcactttgctgg-gacactgattgatgcttctgcctttgtgctgtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 2
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtga-gtgtttttgagggtaacatctgttgctaaatta-cattttc--cat--tcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                                                                               || | || |  |  |  | |  || |   |||  |  |  | || |    | || ||  | |  | |||     | ||  || |||  ||  |||  |||   | |||| ||||| || ||||||||||||||||||||||| | ||| || |||||||| ||||| ||||| || |||||| | ||  | ||| |||| ||||||||
-------------------------------------------------------------------------------gtaggttcactc--tcatccctccctccctccgcctcatcgaatcttttattttgttttgagccaaatccaaacccaacctaacatcatcatcatcatcatcatgcagGCTTCAACGTGGAGAAAGTTCAATACAAGAATGTGGTGTTCACTGTGTGGGATGTTGGTGGCCAGGAAAAATTGAGGCCCTTATGGAGGCACTACTTCAA

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G113995_T03 (Zea mays), 3'ss of exon 2
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagt--gtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                                                                                   |  | |   |  |   |  |     ||||||||  | ||| | |       |||    | ||  ||   ||  |   ||  | |    | | ||    ||| ||||| || |||||||||||||||||||||||   |||||| |||||||| ||||| |||||||| || ||| | ||  ||||| |||| ||||||||
----------------------------------------------------------------------------------ttcctgtcttaattgaaaggcagggctcctgccat-tacatttaaaacaaactttccctgcaaattcgtctgtgacgatatgtctctggtgctatcactagGTTTCAACGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTGTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                                                                             |   | | || |  || |||  |   | |||     | ||    |  ||  |   ||||   | ||  ||   ||  |   ||  | |   || | | |   ||| |||||||| |||||||||||||||||||||||   |||||| || ||||| ||||| |||||||| || ||| | ||  ||||| |||| ||||||||
-----------------------------------------------------------------------------ccaatatgttcttaaaggttttatgaggatt----actaaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 2
gtaatttgacttatcacttgtagtcaatcct-tcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                        | ||  |  ||  | | || | ||||   || |   || ||  |  |      ||  ||| |   |||| |  | ||||  |    |||||||      ||  | || ||     | | | || | | |  | |  |     |  ||   ||| | ||| |||||||| ||||| ||||||||||||||||| | ||| || |||||||| ||||| ||||| |||||  |  | || |||||| |||| ||||||||
---------------------gtccgattgtaccacctatctgcttgtgcatttcataacttttggtttca------accattgctaattacagttgtccaactctgca-cctgcca------tgcaattgattcgtccgttcatatgtttagtgacagcatgcactttatcacattgt-agGTTTCAATGTTGAGAAGGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAA

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccg--tatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                                                                              ||    | ||||   | |||   |||  | ||   |       |||  ||||| |   | | | |    |  |||  ||||||  || || |       || |||| |||||||| ||||||||||| || |||||||||   || ||||| ||||| |||||||| ||||||||| |  | || || ||| |||| |||||  |
----------------------------------------------------------------------------gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtctacataatgtttctctaggtttttaaatt-tatattgc------cttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttg--caaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                                                                            | |     | ||||   | |||  |   | | ||   |      ||||  ||||| |   |   | |    | ||||  ||||||  || || |       || |||| |||||||| ||||||||||| || || ||||||   || ||||| ||||| |||||||| ||||||||| |  | || || ||| |||| || || ||
----------------------------------------------------------------------------attaagtgtctatatggtattgacctggcttgttagttttggcctgcaaatgagtctacatattgtttctctatgtttataaatt-tatattgc------cttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                                                                  |     || || | |  ||||||  |   ||         | | ||| ||  | | | |  ||  |||   || | |  |||| ||  || ||| | ||    | |     ||||| |||||||| ||||||||||| |||||||||||   ||| ||||| ||||| ||||| |||||||||||| || ||||||| ||| |||||||||||||
------------------------------------------------------------------ttcttgtgacattatacttttatctatgattat-------tgttctgtcattttccttttggttgttt---ggattatgtctgctgacaatttaaacttatgttac-----tcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                                                                                  ||     | | || |  | |  | ||   |     | |  |     | | | | |    |||   | || || |     |||||  |||   |   |||| |||||||| ||||||||||| |||||||||||    || ||||| ||||| ||||| |||||||||||  || | ||  ||||| |||||||||||||
----------------------------------------------------------------------------------gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatctta---caacgggt-ttactgagg---attttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDP05355 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                                                                             |   | |   |  | ||| | ||   |||   | |   |    |     ||  |     |     |||       |  |  | |    | ||   ||    |||| ||||| || ||||| || ||||||||||| |||| ||| || ||||||||||| || ||||| |||||  |||| || ||||||||||||||||||||
----------------------------------------------------------------------------cccagtatcccagcccatgctcca--tgtaccccttattacagcccgaacagaatcccccacacacacaatccacacacacctgcgccctgca---aaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGGACGTGGGCGGCCAGGAGAAGCTGCGGCCACTGTGGCGGCATTACTTCAA

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|208360587|gb|DC930859.1|DC930859
EST:     TCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG                         GGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGG
genomic: TCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCGgtaatttgac ... caattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGG
EST: gi|162172685|gb|FC348066.1|FC348066
EST:     TCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG                         GGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGG
genomic: TCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCGgtaatttgac ... caattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGG
EST: gi|18362447|gb|BJ194517.1|BJ194517
EST:     TCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG                         GGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGG
genomic: TCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCGgtaatttgac ... caattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGG
EST: gi|18365645|gb|BJ197722.1|BJ197722
EST:     TCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG                         GGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGG
genomic: TCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCGgtaatttgac ... caattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGG

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), 33 (downstream exon)
Score: 16

GTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCGgtaatttgac ... caattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA
                        tgctaaa  putative branch site (score: 16)
                                    ttttccattc  putative PPT
                           taaattacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA