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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgatctttctcttagcttgtcttcaagaaattccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgattgtacactctaatggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG

Basic information

species Physcomitrella patens
transcript PP1S450_16V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S450_16V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os07g19460.1 (Oryza sativa), 3'ss of exon 7
gtatgtgatctttctcttagcttgtcttcaagaaattccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgattgtacactctaatggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG
                                |  |  | |     |  |  | | ||| ||  ||  ||||  | |   ||  |  | | ||   |||||  || |   ||||| ||  |||| | ||| || || ||  | |||||| |||||||||||||||| ||||||||||| || ||||| ||| || | ||||  ||    | |
------------------------------gtatgtatctttgagtttatactataccacttccct--atgtttatgttttgctcagccaatgcttactct--tgctacatttgatttttagGGCTATGGTTCCTTTCTGTTGCGAGATCTACCATTTGATGCTATTCAGTTTTGCATATATGAGCAACTTCGAATAGGCTATAAACTGGCG

upper sequence: PP1S450_16V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 7
--------------------------gtatgtgatctttctcttagcttgtcttcaagaaat----------tccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgat--tgtacactctaat----ggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG
                          ||     |||||| | ||  ||| | ||  |   ||          |  |    |    | | ||   | || | | | | |     |  | |  |  |||  | | || | ||      | |  |||||  ||| |||||| ||| || || || ||||||||| ||||||||||||| |||||||| |||||||| ||||| ||| || | ||||  ||    |||
gtatgtgtattctggcatcttatttggttaacaatctttatattgacttctgtttgaaggatgaattactgatttactgttgatctgaggtgtaaattttgttcctattttaaatatatcttgtgataatatccattatatcaccggtttcttttggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG

upper sequence: PP1S450_16V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA20G31020.1 (Glycine max), 3'ss of exon 2
gtatgtgatctttctcttagcttgtcttcaagaaattccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgattgtacactctaatggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG
          || |  ||  |  |   |    | | |   |   | | ||||  |    ||| | ||  |   |||        | | ||   |  ||| |  || | || |   |||| |||| | |||||||||| |  | |||||||||||||||||||||||  | || |||||||| ||||||||  |  | || |  ||   || |
----------ttccattttacaagctatttgaataatgtgtgtgtgtggttaactttagttt-tttgttttaccag--------ccttgacc-tctacttt--tgtttttatgagattgtagGGATATGGATCTTTCTTATTGCGAGATTTACCATTTGATGCTATAGAATTATGCATTTATGAGCAGCTCCGTATTGGGTATAAATTAGCG

upper sequence: PP1S450_16V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G36580.3 (Glycine max), 3'ss of exon 8
gtatgtgatctttctcttagcttgtcttcaagaaattccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgattgtacactctaatggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG
                ||  ||||   |    | |||  ||     |   ||||     ||||  |   |||      ||    | | ||      | | |   | | |  |   |||  |||| | |||||||||| |  | |||||||||||||||||||||||  | || |||||||| ||||||||  |  | || |  ||   || |
---------------ttttacttgctatttgaatattatatataattatatatgctaactttagttttttgttttaccag----ccttgacctctaatttt---gttttaatgagattatagGGATATGGATCTTTCTTATTGCGAGATTTACCATTTGATGCTATAGAATTATGCATTTATGAGCAGCTCCGTATTGGGTATAAATTAGCG

upper sequence: PP1S450_16V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA08G15150.1 (Glycine max), 3'ss of exon 7
gtatgtgatctttctcttagcttgtcttcaagaaattccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgattgtacactctaatggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG
   | |||  ||   | |  |||   || ||    ||   |    |   || | | ||   | ||||||     | |     |  |||  | ||         || |||||   |||  ||||| | |||||||||  |  |  | |||||||| ||||||||||| ||||||||||| || |||||| || || | || |  | |   | |
--gtatgaagttcaccatttcttccttttaatttttttttttggacaaattctattccccatgtctgcaatgatatgctaaatgtttctttggtgt-------tgatctttg-aaatcacagGGATATGGATCTTTTTTGTTGAGGGATTTACCCTTTGATGCTATTCAGTTTTGCATCTATGAGCAGATTCGAATAGGTTATATGCTTGCG

upper sequence: PP1S450_16V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT4G39460.2 (Arabidopsis thaliana), 3'ss of exon 8
gtatgtgatctttctcttagcttgtcttcaagaaattccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgattgtacactctaatggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG
                                   |   | |||| |  |    |    ||||  |     | |      || | ||  ||         ||    | |  ||   ||  |||| |   | || |||||  | |||||||| |||||||||||||| ||||| ||||| || ||||||||| | ||||| |  || ||||  
---------------------------------gttagtaacacttttatagctttttctttaagtctgcattcttttgttgaattttcatgtggtgactta----tttcatttgcttctagGGATACCGGTCCTTCCTTTTGCGAGATTTGCCATTTGATGCTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCC

upper sequence: PP1S450_16V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv18s0157g00180.t01 (Vitis vinifera), 3'ss of exon 7
gtatgtgatctttctcttagcttgtcttcaagaaattccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgattgtacactctaatggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG
          ||||  | || || |  ||| |||  | ||  |   |   | |    ||| |||    ||     |    |  |  | |||| |    | || |  | ||     ||||||||| | |||||| ||  |  | ||||||||||| ||||||||| ||||||||||||| || ||||||||  |  | || |  |||  || |
----------tttcgatgagattat--tcatgaa--tgcagtatattt-ctgtagttcatgtattattat---tggtgcattcatcttgattattt--tttatt--ttttgggagattgcagGGATATGGATCCTTTTTATTGCGAGATTTACCTTTTGATGCTCTCCAGTTTTGCATCTATGAGCAGCTACGGATAGGGTATAAGCTAGCG

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|208398417|gb|DC912346.1|DC912346
EST:     CAGCAGTCAGGCAGATTT-GGCCAAAGAGGGTGTGCGTGGTCTATATGCG                         GGTTT-GGATCTTTCCTCCTTCGAAATT-AC-ATTTGATGCTATC
genomic: CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCGgtatgtgatc ... tgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATC
EST: gi|208350179|gb|DC926120.1|DC926120
EST:     CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCG                         GGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
genomic: CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCGgtatgtgatc ... tgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
EST: gi|67718057|gb|BJ968316.1|BJ968316
EST:     CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCG                         GGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
genomic: CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCGgtatgtgatc ... tgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
EST: gi|100407659|gb|BY991791.1|BY991791
EST:     CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCG                         GGTTTTGGATCTTTCCTCCCTCGAGATTTACCATTTGATGCTATCCAGTTT
genomic: CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCGgtatgtgatc ... tgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
EST: gi|162207066|gb|FC382180.1|FC382180
EST:     CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCG                         GGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
genomic: CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCGgtatgtgatc ... tgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
EST: gi|162187904|gb|FC364478.1|FC364478
EST:     CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCG                         GGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
genomic: CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCGgtatgtgatc ... tgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
EST: gi|162187903|gb|FC364477.1|FC364477
EST:     CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCG                         GGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
genomic: CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCGgtatgtgatc ... tgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
EST: gi|67726554|gb|BJ976813.1|BJ976813
EST:     CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCG                         GGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT
genomic: CAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCGgtatgtgatc ... tgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTT

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), 25 (downstream exon)
Score: 15

GTTGTGAAACAGAGAATGCAGACAGGTCAGTTCCCATCAGCACACTCAGCAGTCAGGCAGATTTTGGCCAAAGAGGGTGTGCGTGGTCTATATGCGgtatgtgatc ... tgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtgcaggaagtgtacttcgattgtacactctaatggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG
                              ctctaat  putative branch site (score: 15)
                                       tcttttt  putative PPT
                                         tttttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgatctttctcttagcttgtcttcaagaaattccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgattgtacactctaatggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA