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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG

Basic information

species Physcomitrella patens
transcript PP1S124_47V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
              |    |   | || | |||        | |  | | |   ||     ||   ||   || ||  |  |    ||  |   |  ||||||| |||||||| ||||| ||||||||||| || ||||| || || |||||||| |||||||| || ||||| || || || ||  ||||||
-----------gtaatccccgatatcccgattcgcgccctcgctcgattgtcgtttccgcacccccttctctc-atccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
---tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
     ||||   |   |||    |   |  |  |   |  || | |||   | |    |||        |||  |   ||    | | ||     |     |||||| || ||||| || || ||||||||||| || |||||||| || |||||||| ||||| ||||| ||||| || ||||| ||  | ||||
gtaatccgatccctccgactcg-tgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 1
tcccgaaggcaaagacatactccacccagcttcattataatggtgaac-tatatatttgtttccttatttaatcg---atgtcttttgc-----tggacctgatcac----agATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
            |  |   | ||  |||  |          | |   | ||||| | ||||| ||| ||  || |   || | |||        ||||  | ||       |||||| |||||||| || || ||||||||||| || ||||| || || |||||||| ||||| || |||||||| || ||||| ||  ||||||
----------gtaatcgcgccccctccaattcgtgcgcttcgattttcctatatttctgtttacttgttctattgcagatatttttcctgattgtggatgttatggtgattagATGCGGACATGGAGGACTACGGGTTCGAGTACTCTGACGAAGAGCCGGAGGAGCAGGATGTCGACATTGAGAACCAGTATTACAACTCCAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtct--------tttgctggacctgatc-acagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
            ||  || ||          |  | ||||| ||    |  || |||      | | |||   ||             ||||||     |  |    |||||| || ||||| || ||||| || ||||| || || ||||| |  ||||||||||||||||||||||||||||||||||| ||| | ||||
--------ttctagctattcttt-tttgatgtattcataatagttggtttcatttttaccaattgacttacaagacactaagtaagtgtttgcttcttttattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA19G17660.1 (Glycine max), 3'ss of exon 1
tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgat-cacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
                 ||| |  |      | ||| |  | ||  | |||  ||||| |       | |   ||      ||| | ||     |    |||||| |||||||| || ||||| |||||||| || || ||||| |  || |||||||| |||||||| |||||||||||||| ||| | ||||
----------------gtacgc-gcttgttgttattgttgttgttgattatgcatttggtgttacgatga--tgaaactaattgtttgattgattgtgtagATGCTGACATGGAGGACTATGGCTTCGAGTACTCTGATGAGGAGCAAGAAGAGCAAGACGTTGATATCGAGAATCAATATTACAATTCAAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 1
tcccgaaggcaaagacatactccacccagcttcattataatgg--tgaactatat-atttgtttccttatttaatcgatgtcttttgctggacctgatc-acagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
    |   |  |   | |  |  ||  |  ||||| ||| | |  |  | | ||  |||||  |    |   |   |      ||||||     |  ||   |||||| || ||||| || ||||| || ||||| || || ||||| |  ||||| || |||||||||||||||||||||||||| ||| | ||||
-tttgctagttatt-cttgtttgacgaa--ttcataatagttggtttcattttaccatttgactttgaagacacaagtaagtgtttgcttctgttattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 1
tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgat-cacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
                       || | ||||  |  |  || |||   ||  ||||| |    |  | |   ||      ||| | ||     |    |||||| |||||||| || || || |||||||| || || |||||    | ||||||||| |||||||| |||||||||||||| ||| | ||||
---------------------gtacgc-gcttgttgttgttgttgattaatgcatttggtgttatgatga--tgaaactaattgattgattgactgtgtagATGCTGACATGGAGGACTACGGTTTCGAGTACTCCGATGAGGAGGAAGTGGAGCAAGACGTTGATATCGAGAATCAATATTACAATTCAAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttcct--tatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
                                  | |  |  |||        || |     |   | |   |      ||| | |      |   |  | ||| || ||| |   ||   |    |  |   |||||| |||||||| || ||||| ||||||||||| || ||||| |  ||||| ||||||||||| |||||||| || ||||||||  | ||||
gtcttgttcttgttttgctatgtctaatcttctactctgaaacaatctagggttcgaaagttcccgaattcgactacttactttgttacgaatcgatagtgttttattgatttgggttttcgatttttgt-gtagATGCTGACATGGAGGACTATGGATTCGAGTATTCTGATGAGGAGCAAGAGGAACAAGATGTTGACATTGAGAACCAGTATTATAACTCTAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 1
----tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
     |  ||| |   | |  |  | | | ||     ||  |  |  |  | | | || | ||||  | ||  |||   |     ||  | | | |  |   |||||| |||||||| |||||||| || ||||| || || ||||| || |||||||| |||||||||||||||||||||||||| ||| | ||||
gtatccttgaaagtgcaaat-tctttctctcatacagatgct--taatttattctgtaatggtttgttaataaaatgatttggaattctttggcattct-gtagATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ29478 (Selaginella moellendorffii), 3'ss of exon 1
---------tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
            || ||   |   |  |||    |  | ||  ||      | |      ||   ||  |   |  | | |   | |   ||| |      |   | ||| || ||||||||||||||||| || ||||| ||||| || || ||||||||||||||||| ||||| |||||||| || || ||  | ||||
gtaagctctcttcgtagcgcagcgctcactagggcgcgatttcttgctcccgcgcttggcat---tgcatggatcctcagtaattcttgcttggtttcgtggtgtatagACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAG

upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 1
--------tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
        ||      ||  || |   | | |    ||    |  |  |   |  ||    ||| |  |   |  | | |   | |   ||| |      |   | ||| || ||||||||||||||||| || ||||| ||||| || || ||||||||||||||||| ||||| |||||||| || || ||  | ||||
gtaagctctcttcgtagcgcag-cgctcgctagggcgcgatttcttgctcccgcgcttggcatt-gcatggatcctcagtaattcttgcttggtttcgtggtgtatagACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAG

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), 29 (downstream exon)
Score: 4

ATGGATTCAGgtttgtgggt ... ctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
                                           acctgat  putative branch site (score: 4)
     tatatttgtttcctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgga