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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgaggactatcttggtaacgagtgtagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag

Basic information

species Physcomitrella patens
transcript PP1S214_34V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G164352_T03 (Zea mays), 5'ss of exon 10
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgaggactatcttggtaacgagtgtagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag
|| |  || ||| |||| || || || |||||  | ||||| ||||| |||||||||||||| ||||||||| ||||||| || || || |||||  |   | ||||  ||   | |      ||| ||    || | |||    | |     | | |         |    || | ||||      | |     |||||                                                            
GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAGgttatt--tatatactatctcaatacc--ttatatttcctacaactgtgctgt-gcataatataatccttgatgctaatttatttatcaacagtagctac--aacat------------------------------------------------------------

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgaggactatcttggtaacgagtg-tagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag
||  | || ||||| ||||||||||| |||||| | ||||| || || ||||| |||||||||||||||||  |||| ||||| ||||||||||| |  |  ||    |  | ||   |  | ||| |  |||        ||      |  |  | |   |   |    ||  ||| | | | ||   | | || ||  |                                                            
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtctt----ggct-taagaattattatttcagtattatacactatgcctatatgaatgtgttt---gtgttggtatgtttctgtatcttctac-ttgaatttc-----------------------------------------------------------

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtac-tcgctttataagattgtagtgaggactatcttggtaacgagtgtagaatcgtgggcttttacata-cagcacaggcttgtctatctgtc-----agatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattgg--tgggacttgcag-----
||  | || || || || |||||||| |||||  | || || ||||| ||||| |||||||||||||||||  |||||||||| ||||| ||||| | ||  ||||    ||| || |    || |  |     || |   ||     ||   | || |     | |    || || | |   ||||     | ||  |||    ||  | ||       ||| ||||   |     |   ||| || | ||     ||| |  ||  |     
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatt-tattattaacgaaatgatacaccaacata----tgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgaggactatcttggtaacgagtgtagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag
||  |||| ||||| || || ||||| |||||||| ||||||||||| ||||||||||||||||| |||||| ||||||| ||  |||| |||||    |   || ||   |  ||     | ||| ||   ||      |  ||||| |   |||  | ||  |   |     || ||| |    | || |                                                                    
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtg---tagaaatcttaagcatatagtatgttttcaat-----tcaaatcgagcattttagc-tattggttattggagtatatttacttgttcag--------------------------------------------------------------------

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 5'ss of exon 9
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactc----gctttataagattgtagtgagg--actatcttggtaacgagtgtagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag
||  |||| ||||| || || ||||| |||||||||||||| ||||| || || ||||||||||| |||||| |||| || ||  |||| |||||          ||| ||  | | |||  | |  | | |||   |    |||||  | | || |   || |  ||   | |||                                                                                          
GTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAGgtttgtctagaatttttacaactttagaaaagtcagtgtctatcttgttagtgttaattagtcgctattcat-taatccgcag------------------------------------------------------------------------------------------

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgaggactatcttggtaacgagtgtagaatcgtgggcttttacatacagcacaggct-tgtctatctgtcagatccgttaaacatgagataactttcattcaa--ttcctacgttattgttttctgatgaa--ttggtgggacttgcag
|| ||||||||||| || || || || ||||| || ||||| || || || |||||||||||||| |||||| |||||||| |  |||| |||||| ||  || |  |  || || | |  || ||||   |    |   ||   | |     | | |  |||  |||        ||||     ||| |  | |     |    |   | ||| | ||  | |  |  ||    | | | |||  |  ||  |   |    |||
GTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAGgtattc-tttgagcattttatactaaa-accatctgtctgtttatcttattgttgatctatgtcaagtacctcacctataacatctaatctccagctttggtcccttttctttggatatcactaaagctgcaaatattgagatctccagattgacctttatcatataaacag

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 9
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgaggactatct--tggtaacgagtgtagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag
|| ||||| || || || || ||||| |||||  | ||||| ||||| ||||| ||||||||||| |||||| |||||||| | |||||||||||  | |  |  |  | ||||    |  | |  ||  | ||  |  ||  || || ||||     ||       || |  ||  ||| | | |||  |  |||   |                                                              
GTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAGgt--ttgtctagt--ggttgtgacaattaattgctattagtggcttgtaaaggatagtgga----tatgagtttcaaattctcatct-tatttcattttggtttgtctc------------------------------------------------------------

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 11
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgagg-actatcttggtaacgagtgtagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag
|| || || || || || |||||||| || ||| | ||||| ||||| || || ||||| || || |||||| |||||||||| |||||||||||  |     |   | |||   ||||     || |||   ||| ||  | ||    |     ||    | || || ||        |  ||||  ||| |  ||                                                                
GTTTATTCAATTCGTGATGCAGCTGCTAATAATGTGAAGCGCCTTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctgattacatattactgtgaattggtaccttttaaacaagcattgataaata--tcttgctgttcaacatagataca---aagtgtctaatctgacaag---------------------------------------------------------------

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|37829837|gb|BJ587849.1|BJ587849
EST:     GAAGAGTNTGGTCGTGAGTGGGCATTGCAGCACATCATTCCCCCAG                         GTGATGGAAAAGATAAACAATCTTCATTATTTGTATCGCATGACGGTACT
genomic: GAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATT-CCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACT
EST: gi|37821365|gb|BJ579431.1|BJ579431
EST:     GAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: GAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|162153520|gb|FC330121.1|FC330121
EST:     TTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: TTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|208392785|gb|DC953682.1|DC953682
EST:     TTGCCGANGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: TTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|18335295|gb|BJ167313.1|BJ167313
EST:     AGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: AGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|37821299|gb|BJ579365.1|BJ579365
EST:     AAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: AAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|37828113|gb|BJ586125.1|BJ586125
EST:     AAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: AAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|162153519|gb|FC330120.1|FC330120
EST:     TGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: TGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|37843689|gb|BJ601697.1|BJ601697
EST:     GCCGAAGAGTTTGGTCCTGAGTGGGCATTGCGGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: GCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|162170520|gb|FC347666.1|FC347666
EST:     TTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: TTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|162179207|gb|FC355672.1|FC355672
EST:     TTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: TTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|37829768|gb|BJ587780.1|BJ587780
EST:     TGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: TGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|37845416|gb|BJ603424.1|BJ603424
EST:     TGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: TGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|162254923|gb|FC431108.1|FC431108
EST:     TGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: TGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|37841224|gb|BJ599232.1|BJ599232
EST:     AAGAGTTTGGTCCTGAGTGGGCATTGCGGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: AAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|162258176|gb|FC433958.1|FC433958
EST:     TTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: TTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
EST: gi|37844214|gb|BJ602222.1|BJ602222
EST:     CGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG                         GTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT
genomic: CGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTT

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), 35 (downstream exon)
Score: 21

GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctt ... ggacttgcagGTGATGGAAAAGATAAACAATCCTCATTATTTGTATCGCATGACGGTACTTGTTGCGATTTCTCTTCTTGCTCCAGTAGTTGGTTCCGAAGCCACTTGCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtactcgctttataagattgtagtgaggactatcttggtaacgagtgtagaatcgtgggcttttacatacagcacaggcttgtctatctgtcagatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattggtgggacttgcag

- - - - - - - - - - - - - - - - - - - - - - -  CGAAGA