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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgattagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG

Basic information

species Physcomitrella patens
transcript PP1S1_526V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 5
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgattagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG
                                           |||||  |          | || ||  | |      || ||   || | ||| |   |    |  ||| ||||| |    || | ||| |||| || ||||| |||||||| ||||||||||| || ||||||||||| |||||||| ||||| |||||||||
-------------------------------------------gtcactttc--------ttgacatttctttaaggaactggattgttgtgcaaaaattaacactcaatatatctcat---gttctacagTCTGTTATCAAGAAGAAGTATGGGCAAGATGCTACTAATGTTGGTGATGAAGGTGGTTTTGCTCCAAACATTCAG

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os06g04510.2 (Oryza sativa), 3'ss of exon 6
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgattagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG
                                                ||  | ||| |    || ||    || | |    || | ||   ||  |    ||   |||   |  |||||  |     |||  | |||| |||||||||||||| |||||||| ||||| || || ||||| ||||| || |||||||||||||||
----------------------------------------------gtgaaaaaaaaaaatcaaccttttcattttgtatctgaaactt---cagaatgtgttatctga---acttctttata-----cagAGTATAATCAAGAAAAAGTATGGCCAAGATGCCACAAATGTGGGGGATGAAGGTGGCTTTGCTCCTAACATTCAG

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os10g08550.3 (Oryza sativa), 3'ss of exon 8
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgattagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatag---atctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG
                                                           |    ||||| | ||  ||| || |  |||   | |    |  | ||||| |    ||   |||    | | ||| |||| || ||||| |||||||| || ||||| || || ||||||||||| |||||||| |||||||||||||||
----------------------------------------------------------gtaattctttcatctt-cattttaaaccttttccccatcttacgtcattgaaaattaattaattttatctgtacagTCTGTTATCAAGAAGAAGTATGGTCAGGATGCCACCAATGTTGGTGATGAAGGTGGTTTTGCTCCTAACATTCAG

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G064302_T01 (Zea mays), 3'ss of exon 8
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgattagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG
                              || || |   | ||   | |||     ||| |  |||  |||| | |  ||||  || |    ||| || | |    | || ||   |  | |     |||    | || ||||| ||||| || || ||||| ||||| ||||| ||||| |||||||| || ||||||||||||
---------------------------gtgagcaact---aatgcatctatt-----gatgtaccttaagtgtgg-accctaggaatgtg---aagtcagaat----gctaaatgcttccgtaca---cagAGCATCATCAAGAAGAAGTACGGTCAGGATGCGACAAATGTTGGGGATGAAGGTGGTTTTGCACCTAACATTCAG

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 8
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgat-tagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG
     |   || ||||||  |  |  |  ||    |||  |   | |  |   | ||| |    |       |    | ||   |   ||| |    | ||||| |    | ||| | |||  || || |||||||| ||||| || || || ||||| |||||||| |||||||||||||| ||||| || |||||||| || |||
-----gttatagttcttttcgcataac-ttactcttttacaaaataaaaaaacaaaaacaaaatagacaaaaggaaaaatcattattattagtggtcataaattgagatgttgatgtgttt--atcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 8
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgattagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG
                                           || |   ||         | ||| || | |   ||  |    ||||| |    | ||||| |  ||| | |  || |  || || |||||||| ||||| || || || || || |||||||| |||||||||||||| ||||| || |||||||| || |||
-------------------------------------------gttatagttcttttcgcataactctctt-taaaatcattattatttagtggtcataaattga--gat-gttgcctgtttatcttacagGCTGTTATTAAAAAGAAATACGGTCAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 8
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgattagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG
|||  ||| ||||| | | | | ||    |  | |||| |    |           | || |   ||        |||||   | |||   | | | |  ||  ||   |  || | ||||| | || ||| |||||||||||||||||||||| |||||||| || || ||||||||||| ||||| || ||||| || ||||||
gta--gcattaattttattattattattatttatattttgtgcattttaccccttgaaatttagttt----aacatattc---acattatcttagggcttatc-atgtttctatttgtttgc-tcttccagTCTGTAATTAAGAAAAAGTATGGTCAAGATGCAACCAATGTTGGTGATGAAGGTGGCTTTGCTCCCAATATTCAG

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv08s0007g03960.t01 (Vitis vinifera), 3'ss of exon 8
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgattagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG
                     |  | ||  | ||||||      |  |  | || |   |  || || |    | | | | |  | ||  |      | ||||    | ||  |    |||| || |||||||||| ||||| || || ||||| || ||||| ||||| ||||||||||| ||||| || |||||||| || |||
--------------------ctcatacatcataaattt----cattgcattcagtac--ttacatttgcaaaatctctcccactgtttggtcttctgctaatt----gctattttctcttgc-ttattcagGCTGTGATTAAAAAGAAATATGGTCAGGATGCCACAAATGTTGGTGATGAAGGTGGCTTTGCTCCTAATATACAG

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|162255467|gb|FC431881.1|FC431881
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|67727546|gb|BJ977805.1|BJ977805
EST:     GGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: GGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|100361970|gb|BY947718.1|BY947718
EST:     CTTTCA-G-AAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTA-TTAANGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGA
genomic: CTT-CAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAA-GAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGA
EST: gi|162180206|gb|FC355523.1|FC355523
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|162275868|gb|FC451429.1|FC451429
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|162279243|gb|FC455790.1|FC455790
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|208374338|gb|DC941151.1|DC941151
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAA
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGA-
EST: gi|162273265|gb|FC449246.1|FC449246
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|162255274|gb|FC431584.1|FC431584
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|100361603|gb|BY966133.1|BY966133
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|162255040|gb|FC430913.1|FC430913
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|100352733|gb|BY945421.1|BY945421
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
EST: gi|162186412|gb|FC362968.1|FC362968
EST:     CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAG                         GCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG
genomic: CCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAG

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: 8

GAATTTATGATTTTGCCCACTGGCGCATCTTCCTTCAAGGAAGCCATGAAGATTGGTTCTGAGGTTTACCATAACTTGAAGgtaatgcagt ... catttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG
                           tattgat  putative branch site (score: 8)
                                     tctctttgcatttttc  putative PPT
         atttattcaagacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgattagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG