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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtcagctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC

Basic information

species Physcomitrella patens
transcript PP1S137_209V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtcagctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                                              || | |  |  | | |   | ||  | ||  ||      ||  |||   | ||   ||| |     | |||   ||  | |||  |     | | |   || |  ||    | | |  |    ||||||| ||||||||||||||||| || || ||||| || ||| |||||||||| |||||||| ||||| ||||| || ||||| ||||| |||||||| || |
-------------------------------------------------------------gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgata-gttgcctattctcttaatgt--taaatttattgcaatgatttccattgaatctttt----tccctcat----tgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC

upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os08g17370.1 (Oryza sativa), 3'ss of exon 5
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtcagctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGC----TGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                | | | |  |  |    |   |   || ||| |    ||||  |     |||   ||| | | |||      ||||  | |||   |||    |  ||||    || ||  |  || | |||   |  |   |  ||| ||    |     | ||||||| ||||| ||||||||||||||||||    |||||||| ||| |  ||||||| ||||| ||||| || ||||| |||||||| || ||||||||||||    
-------------------------------gtgagatatatgtgcacttttttccgatcgttctg---ctctaatgaaatgatcgcagtagctagaaa-----ttgttcagtgtgcacta--gatggagtgc--taatattttgttaccatct---atgcgtccttttgactattctgtcaatttgcagGAGAGTGATATCAAGTGGGCATCTCGCTGGCTGGGATACCTATCTACTGATGACGGATGACCAAATCCACTGGTTTTCCATTGTGAATTCCCTCATGATT----

upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os08g44150.1 (Oryza sativa), 3'ss of exon 4
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtcagctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgt-gcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                                 |  |||  ||  ||   |   | || |      |  |  ||   ||| |  || |   || ||   |||  | || |||  | | | ||  |   ||||     |      ||    ||||   | ||    |||||  ||||||||||| ||||||||||| |||||||||||| | ||  |||  ||||||||||||||   ||  ||||| |||||||||||||| |   | |   |  
------------------------------------------------gtggctttcatccttccct-tttatcatcctttcacct--gtaaattgtatcttctccctaaaa---cagacattaatcagatat-taaacctttctctaatgattta---tcacatgcttgtgctact----gctgttacagGAAAGTGATATCAAGTGGGCTTCTCGCTGGGATGCCTACCTGTCAATGACAGATGATCAGGCTCGCTGGTTTTCCATTGTTAACTCTCCTGTTACCCTGA

upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtca-gctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttg---tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                                                                     | | ||  |   |     |  ||    ||||| | ||||   ||    | | || ||   |  || || |   |          ||  |||||| |   |||| ||||||| ||||| ||||||||||| ||||||||||| || || ||||| |||| ||||||||||||||| ||||| || ||||| ||||| |||||||| || |
-------------------------------------------------------------------------------------tgaatctatcacatgaactgcgt----tgtcaagttacttaacatacattttaaaat---ttgagtttgttttaat--gttttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC

upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G180575_T01 (Zea mays), 3'ss of exon 6
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtca-gctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                                                                     | | ||  |   | |   |  ||    ||||| | |||||  ||    | |||| ||     |   || |           | ||| |||| | | |||| ||||||| ||||| ||||||||||| ||||||||||| || || ||||| |||| ||||||||||||||| ||||| || ||||| ||||| |||||||| || |
-------------------------------------------------------------------------------------tgaatctatcacataaactgcgt----tgtcaagttactaaacatacatttcaaaatttgagttcgttttaatgttttctgatttg-cttggtat-tgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC

upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G039811_T01 (Zea mays), 3'ss of exon 6
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtcagcta-ctagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                                                            | || || | |  |       |  |  || ||  ||  |    || ||  |  ||||||          | |   |  |   |    |  | ||         |    | ||||||| ||||| |||||||||||||| || ||||| || ||  |||||||||| |||||||| ||||||||||| || ||||| ||||| |||||||| || |
---------------------------------------------------------------------------gtacgagactgagatta---agaactgcttagtttaactttgtttagctgctgtagtgtact-------ctttgaatgtttatatgtgatgatttcatggaacctcaattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC

upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G146951_T01 (Zea mays), 3'ss of exon 6
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtcagctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                                       ||| | |  ||||  |||  ||   | |||  |      |||   |  |   |  | |   |  |       ||||| | || ||  ||| |   ||   ||   |        |   | || |    | || |||| || |||||||||||||||||||| ||||| |  ||| | ||||||||||||||||| || || |||||||| ||||| || || ||||||||||| |
---------------------------------------------------gtcagaactat-gtttgattcttttt---gtattccaaataagtgattgtagtagctgtagtactaagtgtcctataagtggagcatgaatattgtgttttgctcatttctga-----gaactactgtaaatt-tgtagGAGAGCGACATCAAGTGGGCATCTCGGTGGGACAGCTATCTATTGATGACAGATGATCAGATCCACTGGTTCTCTATTGTGAATTCTCTCATGATTGTTC

upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtc-agctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                                                            | |  || |    |        | || |||  |   |||  |||| |||||  | | | | ||  |   | | |  ||   |    ||     |||         |  | | ||||| ||||| ||||||||||| || |||||||| || ||  |||||||||| |||||||| ||||| ||||| || ||||| ||||| |||||||| || |
---------------------------------------------------------------------------gtacaagactgggattaagaattgcttattttaactttgtttagctgctagtgtactctttgaatgtttcttttg--tcatgattttaa-----tggaacttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC

upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgt-agaatgtcagctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                                                                                   |||  |  | | ||| |  ||||| | | || | |  |   ||   |   | | |   |   ||||    | | |  |||| |      ||||||||||| ||||| |||||||| || ||||| |||||| | || ||||  |||||||| || || |||||||||||  ||||||| || |||||||| |
-------------------------------------------------------------------------------------------------gtattgctgattaaaatcttggctaccaataaactttcacctcatttgttatgatacgttatggcaagtttgttggt-acttttt------cagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC

upper sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA07G01240.1 (Glycine max), 3'ss of exon 6
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgt-agaatgtcagctactagtcaagtgt-atcaagatcattcta-gcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC
                                                                                                   |||  |  | | ||| |  ||||||  | || | | | |    ||||| || | | |   || ||||  | || | | |  || |    | ||||||||||| ||||| |||||||| || ||||| |||||| | || ||||  |||||||| || || |||||||||||  |||||||  | |||||||| |
-------------------------------------------------------------------------------------------------gtattgctgattaaaatcttggctactcataaattttcacctcattcattatatgatacgttaagccaa--agtttgttggtatttt----ttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTTTGATGATTGTTC

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|162192186|gb|FC368335.1|FC368335
EST:     AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAG                         GAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
genomic: AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAGgtgggtgatt ... tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
EST: gi|162155481|gb|FC331484.1|FC331484
EST:     AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAG                         GAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
genomic: AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAGgtgggtgatt ... tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
EST: gi|162159734|gb|FC336120.1|FC336120
EST:     AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAG                         GAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
genomic: AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAGgtgggtgatt ... tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
EST: gi|162156308|gb|FC332332.1|FC332332
EST:     AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAG                         GAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
genomic: AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAGgtgggtgatt ... tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
EST: gi|100433575|gb|BY960600.1|BY960600
EST:     AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTTGTTTCAG                         GAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
genomic: AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAGgtgggtgatt ... tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
EST: gi|100374433|gb|BY985788.1|BY985788
EST:     TATGATGTGTCGTTTCAG                         GAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
genomic: TATGATGTGTCGTTTCAGgtgggtgatt ... tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
EST: gi|100389535|gb|BY989013.1|BY989013
EST:     AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAG                         GAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA
genomic: AGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAGgtgggtgatt ... tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACA

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), 33 (downstream exon)
Score: 32

CTGCAACCCCAACACCAGGACTTATGTGACATATGGTCAGGACCCCCAGGAGTTAGTTGAAGGCCATGAAGTGGTTTTCACTTATGATGTGTCGTTTCAGgtgggtgatt ... tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC




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