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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacacatgccttttatgttggaacgaattgtttctttaaatgtaaaagaatcctgcggatttacactaacatgcacttttctgtatgtcatccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG

Basic information

species Physcomitrella patens
transcript PP1S1_304V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
gacacatgccttttatgttggaacgaattgtttctttaaatgtaaaagaatcctgcggatttacactaacatgcacttttctgtatgtcatccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG
                ||| |  |   |     | |||     |   ||||  |||    ||      | | || | |   | |   |  ||  |   ||| || ||||| ||||| ||    || |||||||||||||| ||||| ||||||||||||||||| || ||| |||| || || |||||||| || || ||
----------------gttagccctcctcaa--ccttatgcccatttgaat--tgcttcattctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG

upper sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G328578_T01 (Zea mays), 3'ss of exon 2
gacacatgccttttatgttggaacgaattgtttctttaaatgtaaaagaatcctgcggatttacactaacatgcacttttctgtatgtcatccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG
                ||| |  |   |     | |||     |   ||||  |||    ||      | | |  | |   | |   |  ||  |   ||| || ||| | ||||| ||    || |||||||||||||| ||||| ||||||||||||||||| || ||| |||| || || |||||||| || || ||
----------------gttagccctcctcaa--ccttatgcccatttgaat--tgcttcattctgaggatacgtccctgattattattgttctatattagGCTACATTAGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG

upper sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G083497_T04 (Zea mays), 3'ss of exon 1
gacacatgccttttatgttggaacgaattgtttctttaaatgtaaaagaatcctgcggatttacactaacatgcacttttctgtatgtcatccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG
           ||  |  |  | |   |      ||| ||| |   || || | | ||||    ||          ||     ||| | ||       |||||| ||||| ||||| ||    || |||||||||||||| ||||| || |||||||| |||||||| ||| | ||||| |||||||| || || |||||
----------gttagttctcaatctcgtgccccatttcaat-tggcagcattccgaggatacgtacc------tgattagtgctatattatt------agGATACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATTGTGGTGGAACTGAACGGCAGACTAAACAAATGCGGTGTAATTAGCCCCCG

upper sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G38520.1 (Glycine max), 3'ss of exon 2
gacacatgcctttta-tgttggaacgaattgtttct-ttaaatgtaaaagaatcctgcggatttacactaacat-gcacttttctgtatgtcatccctcg--cagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG
     ||  || | | |  |  ||    || ||| | ||   |||  ||  ||  |  |  | |  | | | || |   || | |    || ||   | |   |||||| ||||||||||||||    |||||||||||||| || || ||||||||||| ||  ||||||||||| |||||||||| || ||||| ||||||||
---gtatatctctcagtaatcaaagtttttatttttattttctgtttaattattata-gtttgtgtattgaaattgttgttgtgttcgggtgattttttgtttagGATACATTGGAGAGTTTGAGTATGTTGATGACCACAGGGCTGGTAAAATCGTGGTTGAATTGAACGGTAGACTGAACAAGTGTGGGGTTATTAGTCCCCG

upper sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 2
gacacatgccttttatgttggaacgaattgtttctttaaatgtaaaagaatcctgcggatttacactaacatgcacttttctgtatgtcatccct-cgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG
     ||  || |||      || |  ||| || | | | | ||     ||   |    | ||    || ||||  || | |     | ||   |  | |||||| || |||||||||||    |||||||||||||| || || ||||||||||| ||  ||||||||||| |||||||||| || ||||| ||||||||
---gtatatctcttagtaatcaaagttttgattttattatt-tatttttatttagtttgtgtattgaaaaatgctgttgtgttcggatgatttatgtgtagGATACATCGGAGAGTTTGAGTATGTTGATGACCACAGGGCTGGTAAAATCGTGGTTGAATTGAACGGTAGACTGAACAAGTGTGGGGTTATTAGTCCCCG

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|162218720|gb|FC394270.1|FC394270
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|18373221|gb|BJ204823.1|BJ204823
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|18356753|gb|BJ188812.1|BJ188812
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|67576889|gb|BJ949713.1|BJ949713
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|162226357|gb|FC403273.1|FC403273
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|162273654|gb|FC449383.1|FC449383
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|67573039|gb|BJ945863.1|BJ945863
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|37843743|gb|BJ601751.1|BJ601751
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|37833696|gb|BJ591708.1|BJ591708
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|162273653|gb|FC449382.1|FC449382
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|162202882|gb|FC379864.1|FC379864
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|162194896|gb|FC370547.1|FC370547
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|67700425|gb|BJ960658.1|BJ960658
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|67696421|gb|BJ956654.1|BJ956654
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|162218719|gb|FC394269.1|FC394269
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|162269511|gb|FC445067.1|FC445067
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|162226443|gb|FC402423.1|FC402423
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
EST: gi|162202881|gb|FC379863.1|FC379863
EST:     CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACG                         GATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG
genomic: CCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCG

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), 35 (downstream exon)
Score: 43

AAGAACATGTTCAACGCTGAGAAGCGCGGCAAGAGGCAGGTGCTCATCCGCCCTTCCTCCAAGGTTGTCATTAAGTTCCTCTCCGTCATGCAGAAGCACGgtgagaacgt ... tccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaatcctgcggatttacactaacatgcacttttctgtatgtcatccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG
                  cactaac  putative branch site (score: 43)
                                          tcatccctc  putative PPT
             atttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacacatgccttttatgttggaacgaattgtttctttaaatgtaaaagaatcctgcggatttacactaacatgcacttttctgtatgtcatccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- cacatgc