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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT

Basic information

species Physcomitrella patens
transcript PP1S138_36V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 8
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
                                                                    ||  |   || |||   |    ||||    |  | | |  || |  ||  |   ||          |    |   |         |||| ||| | |||   |||||| ||| ||||||  |||| ||||| ||||| ||||| |||||||| ||||||||||| ||||| | || ||| || ||  
--------------------------------------------------------------------gtaagtgcaattttctgtgcttcatcccttttgaggaagttccgtcaactaatggtgaagactaaaatctataatttttattgaaagGTGAGCCTTGTGCAAATTCCTGGCAAAGAGGAGCTGCGGCAGAAAAACCTTTTCAGTGTCAGTGATTGCAAGATGTACTGGCAGAACAGTGGAGAATATC

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 8
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
                                          |||  ||||     || ||||| ||      ||| |    | ||   |||| || ||  |   ||||   |  |||| | |    | |   |      || || |      |||| ||  | |||   || ||| ||| ||||||  |||||||||| ||||| ||||| |||||||| || |||||||||||||||| || ||| || ||  
------------------------------------------gtg-agcat-----aaatttgtgga------acagatacctcttataccatgtttattca-ataact--aatgataa-aggctaaaattgatcttttctgttgaa------agGTGAGTCTAGTGCAAATCCCTGGCAAAGAGGAGCTGCGACAGAAAAACCTTTTCAGTGTCAGTGATTGTAAGATGTATTGGCAAAACAGTGGAGAATATC

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 11
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcgga--gtgcttacggcttgctgcatcctt-cagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
                     | | ||||||| |  |||    ||| |   |  ||||||||                |||||| ||||  ||  | ||| |||    | |   | | || | |       |  ||| |   |    |||  ||  |||||||  || |    || || |||| ||||||| |  | ||||||||||| ||||| ||| |||||||||||||||| |||||||||||||| || ||| 
--------------------gtaagtatgtattttttctttcatgtaggtctattgaagtttt---------------attttacttggttattgtaatgaatggtcatatattatttattaattattttatatttatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCGGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatcctt-cagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
                            ||| ||    |    | |  |||   ||  ||||    || |  |      ||||| ||||  ||| | ||| |||    | |   | | || | |     |   || |   |    |||  ||  |||||||  || |    || || |||| || |||| |  | ||||| ||||| ||||| |||||||||||||||||||| |||||||||||||| || ||| 
----------------------------gtaagtgtgtttttttctttcatgtatgtggttta--aagttttg------ttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
||  ||||    ||   |||||    |||||  |    ||  || | |  || ||   || |  | | |   |   | || ||||||  | ||  |  | |||  |                       || |      ||| |  ||   | |||||||  || |    || || |||| ||||||| |  | ||||||||||| ||||| ||||||||||||||||| || |||||||||||||| || ||| 
gtaagttt--gtctttttcttt---catgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatcta-----------------------tgttc----tttgatatatttat-agGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 8
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
               |  |     ||   |    || |     | |    ||  |  | |||| |    | |    ||    ||||| ||     |    ||  ||| |   ||  | || | |    ||  ||||   ||  |  |   | ||||| ||  ||||    || || || | |||||| ||| | |||||||| ||||| || || ||||||||||| ||||| |||||||||||||| || ||| 
-----------gtgagtgcagctgttccatgcaaaaccagttttctcttctttttatattttgcttctcttcctttaa----tattttgcttctcttccatagacaagttaaaatttgattaat---ggtctttac---ttcataaaatatgcagGTGAGTCTGGTTCAAATCCCCAGTAAAGAGGAGTTGAGGCAGAAGAATCTCTTTAGTGTTAGTGACTGCAAAATGTACTGGCAAAGCAATGGGGACTACC

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ13839 (Selaginella moellendorffii), 3'ss of exon 8
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
                                                                                       |    | ||  ||| || |  |||  | ||  | |   ||  ||||   | |||        |  ||||||||| ||||    |||||| |||| || ||| || | ||||||||||| ||||| |||||||||||||||||||| ||||||||||| || || ||  
---------------------------------------------------------------------------------------gtatgtatttgtgtttg-atttctctacatg-tgacctggtttgctcttgactt--------caacagGTTAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATC

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ12681 (Selaginella moellendorffii), 3'ss of exon 8
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
                                                                                       |    | ||  ||| || |  |||  | ||  | |   ||  ||||  |  |||        |  ||||| ||| ||||    |||||| |||| || ||| || | ||||||||||| ||||| |||||||||||||||||||| ||||||||||| || || ||  
---------------------------------------------------------------------------------------gtatgtatttgtgtttg-atttctctacatg-tgacctggtttgctctcaactt--------caacagGTCAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATC

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|162213005|gb|FC389221.1|FC389221
EST:     TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGG                         GTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
genomic: TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
EST: gi|162172466|gb|FC349135.1|FC349135
EST:     TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGG                         GTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
genomic: TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
EST: gi|162170163|gb|FC347283.1|FC347283
EST:     TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGG                         GTTAGCTTGGTGTCCATTCCTAGCAG
genomic: TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAG
EST: gi|162186685|gb|FC363657.1|FC363657
EST:     TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGG                         GTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
genomic: TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
EST: gi|162154476|gb|FC330478.1|FC330478
EST:     TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGG                         GTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
genomic: TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
EST: gi|162154708|gb|FC331646.1|FC331646
EST:     TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGG                         GTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
genomic: TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
EST: gi|162171931|gb|FC349029.1|FC349029
EST:     TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGG                         GTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
genomic: TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
EST: gi|162179642|gb|FC355700.1|FC355700
EST:     TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGG                         GTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
genomic: TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
EST: gi|162230691|gb|FC406114.1|FC406114
EST:     TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGG                         GTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC
genomic: TGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTC

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: 28 (upstream exon), 34 (downstream exon)
Score: 5

ATTGAAGGTGGAGAATGTGGTCGATTTCTGTTGGTCACCAACCGACCCACTGTTGTCCCTCTTCGTTCCTGAAGGTGGTGGTGGCAACCAGCCTGCCAGGgtgggtttcg ... catccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
                             tgcttac  putative branch site (score: 5)
                                             catccttc  putative PPT
        tctgaaaataataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA