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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatggattggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag

Basic information

species Physcomitrella patens
transcript PP1S450_22V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os01g13770.3 (Oryza sativa), 5'ss of exon 2
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatggattggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag
||||||||||||||| || ||||||||| | || |||||||| |||||||| || ||||| || ||||||||     |||    ||   |||  | |     ||||| || || ||        | |  ||    | |  |||   | | |  ||      |   | ||     |     |  |||  |  ||                                                     
GTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATAgtaagt-----gtattattgttcttccccccttgctttgcaacagtgagcatcagcaagctgcgtgatcttgcattccattttgtagctgggttacgacatagtatgaacaatcgtactgcttgctgcag--------------------------------------------------

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G070605_T01 (Zea mays), 5'ss of exon 3
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatgg-attggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag
||||||| | |||||||| ||||||||| | |||||||||||||||||||| || ||||| || ||||||||   ||   |        || ||   | | | | ||  | |    || |      |    |||| ||||    |                                                                                                      
GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggcaaacctggcaggcttgatt--aattgattcataaatagatgaggaccaacaacattttgctcgttgcag------------------------------------------------------------------------------------------------------

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA13G24360.1 (Glycine max), 5'ss of exon 3
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatggattggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag
||||||||||||||| || ||||||||| | ||||||||||||||||| || || ||||| || ||||||||  | ||    | ||  | |  ||    | || |  |  ||     | | ||    ||  |||||  |  | |||  |   ||    |     ||                                                                                
GTACTTCTTGAACGTGATTTTCAACATCCTTAACAAGAAGATCTACAATTACTTCCCCTATCCATAgtaagttat-agcgattatgtgtattttcaactttgt-gtggtgttagctcatgaatttcatgtcttgatgttaattgtgattggatccgtgaaatgttatg------------------------------------------------------------------------------

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G32190.1 (Glycine max), 5'ss of exon 3
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatggattggtttgatcgtcttcgtgtatatct-ctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag
||||||||||||||| || ||||||||| | ||||||||||||||||| || || ||||| || ||||||||  |   ||    |  |||  ||    ||| || || | ||| | |  ||      | | |  |||   ||| ||| |   |  |||  || | | || | ||||  |                                                                    
GTACTTCTTGAACGTGATTTTCAACATCCTCAACAAGAAGATCTACAATTACTTCCCCTATCCATAgtaagttatagctat---tatattatat----gtattttcaactttgtgtggtgt------tagctc-atcaatttcatgtcttgatgttaattggaattggatctgtgaaata-------------------------------------------------------------------

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 3
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatggattggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag
|||||||||||| || || ||||||||| | |||||||||||||| || || || || || |||||||||||  | |     | |   |||    | | |  ||  ||  ||    | |   |    |  |||||||  |  | | ||| ||| |       | |                                                                                 
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttcttacacatttttatttttggattaatgttttaagagttaattgcaaattttcatattttgatctacaacttatat-tctgtggtcctaatttt-------------------------------------------------------------------------------

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 3
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttg-cagcattgcgcgaagtatgga-ttggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag
||| ||| | ||||| || ||||||||| | |||||||||||||||||||| || || || || |||||||| |     |  |      |  || | ||    || | |     |  |  | ||||| ||| |   |     ||  ||    ||| |     |  ||  ||                                                                             
GTATTTCCTCAACGTTATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCATATCCTTAgtaagtatggctaaaattcttggtatatatgagcttctgacggtccatctgggggcatggaattgatgaaagttagtttatggtggtctgtggggtgt-gtgcag-----------------------------------------------------------------------------

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ15759 (Selaginella moellendorffii), 5'ss of exon 3
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatggattggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag
||| ||  | || || |||||||||||| | ||||||||||||||||| |||||||| || || |||||||       |||||| ||      |  ||    ||  | |||  |  ||   ||| | | |||   | |                                                                                                            
GTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATAgtaagc------tacctcagc------tgacaaggtttttatcatctcctga--catgaactcgttct-tag------------------------------------------------------------------------------------------------------------

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ38162 (Selaginella moellendorffii), 5'ss of exon 2
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatggattggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag
||| ||  | || || |||||||||||| | ||||||||||||||||| |||||||| || || |||||||       |||||| ||      |  ||    ||  | |||  |  ||  |  | || | | | |                                                                                                               
GTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATAgtaagc------tacctcagc------tgacaaggtttttatcatctcctgacatg-gaatcgttcttag--------------------------------------------------------------------------------------------------------------

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|100367304|gb|BY984874.1|BY984874
EST:     TCTTTCA-CATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCC
genomic: TCTT-CAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCC
EST: gi|67709586|gb|BJ965402.1|BJ965402
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|100397819|gb|BY990417.1|BY990417
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|100384601|gb|BY950591.1|BY950591
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATNTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|67719082|gb|BJ969341.1|BJ969341
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTG
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTG
EST: gi|100449284|gb|CJ973583.1|CJ973583
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGA
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGA
EST: gi|67716735|gb|BJ966995.1|BJ966995
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|208378082|gb|DC932448.1|DC932448
EST:     ATCTTCAACATCATGAACAANAANATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|67704465|gb|BJ964698.1|BJ964698
EST:     ATCTTCAACATCATGAACAAGAAGATCTACNACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTG
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTG
EST: gi|100436251|gb|BY979454.1|BY979454
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTTGGC-GTCGGCGTTGCTTACTGTG
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTT-GGCCGTCGGCGTTGCTTACTGTG
EST: gi|67716900|gb|BJ967159.1|BJ967159
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|67717698|gb|BJ967957.1|BJ967957
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|208392058|gb|DC941906.1|DC941906
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|208360889|gb|DC934785.1|DC934785
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|208369404|gb|DC936093.1|DC936093
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|67717101|gb|BJ967360.1|BJ967360
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTC
EST: gi|67717918|gb|BJ968177.1|BJ968177
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTG
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTG
EST: gi|18361942|gb|BJ194009.1|BJ194009
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCA
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCA
EST: gi|67578440|gb|BJ950607.1|BJ950607
EST:     ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA                         CTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGAT
genomic: ATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGAT

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: 31 (upstream exon), 29 (downstream exon)
Score: 20

GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttc ... ttgcgtgcagCTTTGTCTCTGCTATCCACTTGGCCGTCGGCGTTGCTTACTGTGTGATTTCGTGGATGTTGGGATATCCGAAGCGGGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatggattggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag

- - - - - - - - - - - - - - - - - AAGAAG