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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgttttgcccataaattttaatgtgcatcagttagttttgtttgttacttgttttagtggtgaatgtgatgatttttatgtattctcgcacggaat...

Basic information

species Physcomitrella patens
transcript PP1S44_102V6.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 18
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgt---ctcgttttgcccataaattttaatgtgcatcagttagttttgtttgttacttgttttagtggtgaatgtgatgatttttatgtattctcgcacggaat
 |||||||| | ||||||||| || || || || |||||||||||||||||| | || ||||||||  | || |  |||||    ||  ||   |||  ||||  |   |    || ||  || | |     ||   |  |||  |   |    || ||    |    |||    |      
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgccaatt--ttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt-

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 18
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 17
TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgttttgcccataaattttaatgtgcatcagttagttttgtttgttacttgttttagtggtgaatgtgatgatttttatgtattctcgcacggaat--
 |||||||| || |||||||| || || || || |||||||||||||||||| | |||||||||||  | || ||||||||   || ||        |      |||     |   | |    | |   | || | ||  || |  |  || | ||  || | |  | | |    || |  
ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACATTATTCACTTCAACACATTGGCAAATCAGgtaaggtctttaatgcccacccccctgttttgtaaccaatcaattatcacaatt-tattgttgctccacctgct-atcattgtattgttttgtcaagatttg

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 18
lower sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 17
TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgttttgcccataaattttaatgtg---catcagtta--gttttgtttgttacttgttttagtggtgaatgtgatgatttttatgtattctcgcacggaat
 |||||||| || |||||||| || || || || |||||||||||||| ||| | |||||||||||  | || ||||||||    | |   | |  | |  |  |||      | ||| |  |||||   ||    ||||||| |   |||    |   | || | |  | |   |   |    
ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctcaactagcagtacttctgtaatttttgagtaaatgtttttcctgcagattgtttt-gcaatgatcaaggaaacttat-taaacttctgattgt---

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 18
lower sequence: GRMZM2G128877_T04 (Zea mays), 5'ss of exon 1
---------------------TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgttttgcccataaattttaatgtgcatc---agtta--gttttgtttgttacttgttttagtggtgaatgtgatgatttttatgtattctcgcacggaat
                      |||||||| || |||||||| || || || || |||||||||||||| ||| | |||||||||||  | || ||||||||    | |   | |  | |  |  |||   |    ||| |  |||||   ||    ||||||| |   |||    |   | || | |  | |   |   |    
ACAAGTGTTGTTTAATATTAGATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctcaactagcagtacttctgtaatttttgagtaaatgtttttcctgcagattgtttt-gcaatgatcaaggaaacttat-taaacttctgattgt---

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 18
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 18
TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgttttgcccataaattt-taatgtgcatcagttagttttgtttgttacttgttttagtggtgaatgtgatgatttttatgtattctcgcacggaat
 ||||||||||||||||| || || ||||| || |||||||||||||||||| |||| ||| ||| | | || |||||||| | ||  ||     ||      | | |       ||  |||    |   |        |   ||  |||| || |||   || ||   ||         
ATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAGgtatggtagtgtaaggaatcaggcagtttttggtgttttatttatactagaaaaaagaagaaaagtccatgtaatcattggcatctaggttcaagttact-

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|37836831|gb|BJ594839.1|BJ594839
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37838710|gb|BJ596718.1|BJ596718
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|162276207|gb|FC452899.1|FC452899
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37845049|gb|BJ603057.1|BJ603057
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37838267|gb|BJ596275.1|BJ596275
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|22131932|gb|BQ826891.1|BQ826891
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|18337399|gb|BJ169423.1|BJ169423
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37852823|gb|BJ610831.1|BJ610831
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|15327219|gb|BI487765.1|BI487765
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37848114|gb|BJ606122.1|BJ606122
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|162276206|gb|FC452898.1|FC452898
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|67578993|gb|BJ951144.1|BJ951144
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37834888|gb|BJ592900.1|BJ592900
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|162186096|gb|FC361300.1|FC361300
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37846602|gb|BJ604610.1|BJ604610
EST:     GGTGTGGATGATGCGCAACATTGTCCACTTCAACACTTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: GGTGTGGATGATGCGCAACATTGTCCACTTCAACAC-TCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|162258844|gb|FC434851.1|FC434851
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37853133|gb|BJ611141.1|BJ611141
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37822114|gb|BJ580180.1|BJ580180
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37834988|gb|BJ593000.1|BJ593000
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|162239653|gb|FC418014.1|FC418014
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37848974|gb|BJ606982.1|BJ606982
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|37850336|gb|BJ608344.1|BJ608344
EST:     GGTGTGGATGATGCGCAACATTGTCCACTTCAACACTTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: GGTGTGGATGATGCGCAACATTGTCCACTTCAACAC-TCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
EST: gi|162179502|gb|FC356542.1|FC356542
EST:     CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG                         GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC
genomic: CGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATC

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: 34 (upstream exon), 31 (downstream exon)
Score: 29

TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgtctcgtttt ... ctgtctgcagGCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT




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