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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG

Basic information

species Physcomitrella patens
transcript PP1S66_174V6.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 14
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctg----cagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
            ||   | |   |  | |  |  ||  | |||  ||| |   | | ||  ||    |        |||    | ||| |         |||| |  |||| |       |   | | |  |   || | |  | ||  |    ||| |||   |    | ||  ||| |  ||  | ||     |||| || |||||||||||||||||||| || || ||||| ||  | |||||||| | ||||| |||||||||  ||||||| || ||||||||||| ||||
------------gtacgttgacgtgctcagaaggctggcctttgctttgaatcg-tctactatccagg--------aaaaaacatatcgacatgccttgatattgctgactctcaagaacatagcttcaagaaaaacatatgct-gaaaacagcatt-gttaaacttggttcttatttttaatgtttttggttttagGTTGTGGAGCTTGACTTCTTGTATCCAAGTGAGGGTATCCATCGACGATGGGATAATGGATTTCGCATCACGGCTACTGCAGCTACATGGGATCAGGCAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 7
gtgattaaaaccgtcgat-cggtttttttattaaactttcatttatttttatcagctttatg-attttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgatta-tgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
     || |   ||   | ||   ||  | ||||   | ||     ||  |   | |  |   |   | | | ||||    |   |  | |||   |  | | ||  | || | | |||         ||   | | ||     ||  |||| ||          || |  || |   ||||| |||       |||| || |||||||| ||||| ||||| || || || || |||| ||| ||||||| ||| |||||||||||  | || |||||||||||||| || ||||
----gtatatgtgttactgcgcccttggtcttaagtgtccacaaccttacagtggatagaaatagactggta-gatctgctg---aagttaatctggcaaga-atttaagattatatgaaaatggggattgagaattacaaaggttccattactgaagcacaacactgagcataccaatttctcttgt------agGTAGTGGAGCTTGATTTCTTATATCCGAGTGAGGGCATCCACATGCGTTGGGACAATGGCTATCGCATCACGGCAACGGCTGCCACATGGGACCAGGCAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 14
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggact--ttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
                                                                                            |      || |  |  | |  ||||||   || | | | |  |    |        |  || | || || ||     | |    |     ||     |   |||| || || ||||| ||||||||||| || |||||||||||  |  | ||||| | ||| ||||||||||| || |||||||| |||||||||||||| |
--------------------------------------------------------------------------------------------gtcttgtatttaaaaaattaattgtgattaaatatccttgtggcactg-------aaaaatcccatctgatttatgtattctctccaaacttaatgcc---agGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAATGGTTATCGCATCACCTCAACTGCTGCAACATGGGATCAAGCTG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
                                                                                 ||     | || | | |   ||  |     ||||||   || | | |         |||    |||  |  | || || ||     | |    |     ||     |   |||| || || ||||| ||||||||||| || |||||||||||  |  | ||||| ||||| ||||||||||| || |||||||| |||||||| ||||| |
---------------------------------------------------------------------------------gtcttgtattttaaaaa---attaa-----ttgtgattaaatatcct--------tgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgcc---agGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA06G09190.2 (Glycine max), 3'ss of exon 14
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggact--ttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG-----------------------------
                                                                                            |      || |  |  | |  ||||||   || | | | |  |    |        |  || | || || ||     | |    |     ||     |   |||| || || ||||| ||||||||||| || |||||||||||  |  | ||||| | ||| ||||||||||| || |||||||| |||||||||||||| |                             
--------------------------------------------------------------------------------------------gtcttgtatttaaaaaattaattgtgattaaatatccttgtggcactg-------aaaaatcccatctgatttatgtattctctccaaacttaatgcc---aggttgtggaacttgatttcttgtatcccagTGAAGGTATTCATCGAAGGTGGGATAATGGTTATCGCATCACCTCAACTGCTGCAACATGGGATCAAGCTGCTTTTGTTCTTAGTGTCCCAAGAAGAAAA

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 14
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
                                                                                         ||||      |  |  |    || ||    ||   | |    | ||     |  | || |    ||||   |   ||      | | |  || ||  | | ||||||||||| || || ||  |||||||||| || || ||||||| ||| |||||| |||| ||||| |||||| |||||||||| || ||||| ||||| |
-----------------------------------------------------------------------------------gtgattattggactgaactttcatctgttagtagtttagttcat----aatgcaacttcatagaatgaa-tattgagtctcca------ttcatgtttatgaattt-cagGTGGTTGAACTAGATTTTCTGTATCCTAGTGAGGGGATTCACAAGCGTTGGGACTGTGGGTATCGAATCACAGCTACTGCTGCAACTTGGGACCAAGCTG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 14
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
                                                                               |||   || | ||    |||  | |    | |  || |  |      ||   | ||     |  | || |    ||||   |   ||      | | |  || ||  | | ||||||||||| || || ||  | |||||||| || || ||||||| ||| |||||| | |||||||| |||||| |||||||||| || ||||| ||||| |
-------------------------------------------------------------------------------gtgattattatttattggactgaactttca-tccgtcaattgtttagttcataatgcaacttcatagaatgaa-tattgagtctcca------ttcatgtttatgaattt-cagGTGGTTGAACTAGATTTTCTATATCCTAGTGAGGGGATTCACAAGCGTTGGGACTGCGGATATCGAATCACAGCTACTGCTGCAACTTGGGACCAAGCTG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggact--ttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
                                                                                            |      || || |  | |  ||||||   |  | | |         |||    |||  |  | || || ||     | |    |     ||     |   |||| || || ||||| ||||||||||| || ||||| |||||  |  | ||||| ||||| ||||||||||| || |||||||| |||||||| ||||| |
--------------------------------------------------------------------------------------------gtcttgtatttcaaaaattaattgtgattaattatcct--------tgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgcc---agGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 12
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgc-tatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
                                                                                                                                    || |     ||  |  |  ||  | ||||||   |||  |||   | | ||        ||||| || ||||| || ||| | ||||| |||||||| || ||| |||| |||||  ||||||||||||||||  | ||||| || || |||||||||||||
--------------------------------------------------------------------------------------------------------------------------------gtctgttaatccattcgggcttcgcacacttgttt--gacagcgctatatgcatta-----cacagGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctt-----tcttttgcctc-tgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
                                                                                                                                               |   |||  | ||| |    || ||    || ||        | ||| |    ||||| || ||||| || ||| | ||||| |||||||| || ||| |||| |||||  ||||||||||||||||  | ||||| || || |||||||||||||
----------------------------------------------------------------------------------------------------------------------------------------------gtctgttaatccattcgggcttcgcacacttgtttgacagcgctatgcatgacacagGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG

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|162176121|gb|FC351889.1|FC351889
EST:     GAAGCCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAG                         GTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGG
genomic: GAAGCCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAGgtgattaaaa ... gcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGG
EST: gi|162165454|gb|FC342021.1|FC342021
EST:     GAAGCCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAG                         GTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGG
genomic: GAAGCCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAGgtgattaaaa ... gcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGG
EST: gi|162189086|gb|FC365204.1|FC365204
EST:     GAAGCCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAG                         GTGGTTGAGCTTGACTTCTTGTATCCTAGCNGA-GGTATTCACAGGCGATG
genomic: GAAGCCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAGgtgattaaaa ... gcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGC-GAAGGTATTCACAGGCGATG
EST: gi|162194954|gb|FC369032.1|FC369032
EST:     GAAGCCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAG                         GTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGG
genomic: GAAGCCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAGgtgattaaaa ... gcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGG
EST: gi|162176120|gb|FC351888.1|FC351888
EST:     CCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAG                         GTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGG
genomic: CCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAGgtgattaaaa ... gcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGG

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), 34 (downstream exon)
Score: 12

CAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGCTACTGCGGGAAGCCGATGGGGTGTCGTTATGTCTCGAAATGCAGGGTTCTCAGACCAGgtgattaaaa ... gcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG
                      ttctcac  putative branch site (score: 12)
                                 ctgctttcttttgcct  putative PPT
               tatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC