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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtccatgaactcatttgattcacagttgctgctgaaccttttaattcccagctaggatccttgatttaccaatcaatattcgtcacgtcttgctatcgattgctgtgtattcctaaaacaactggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG

Basic information

species Physcomitrella patens
transcript PP1S35_94V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
gtgagtccatgaactcatttgattcacagttgctgctgaaccttttaattcccagctaggatccttgatttaccaatcaatattcgtcacgtcttgctatcgattgctgtgtattcctaaaacaactggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG
                                                                            | | |      ||  | ||  | |  ||   ||  |     |    ||||  | ||||    |     ||||||||||||||||||||||||| || || || || ||||| ||| |||| ||||| ||||| || || |||
---------------------------------------------------------------------------gtaagtgacgagca--ttttattgtttatgaatggattgcatttgctcaac--gctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG

upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 13
gtgagtccatgaactcatttgattcacagttgctgctgaaccttttaattcccagctaggatccttgatttaccaatcaatattcgtcacgtctt-gctatcgatt--gctgtgtattcctaaaacaac-tggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG
                                                      |  || ||  |    |||    ||   | | |   |||||| | || |  ||  || || ||     ||    || || |   ||         ||||||||||||||||||||||||| || || || || || || ||  ||||||| || || || ||||| |||
------------------------------------------------------gtgagtataatgatattatttttcttcacttggttcgtctttgttagcctttcagcagtataacttgaatttgacatgatcactcccaccacgcagGACATCAAGTTTGCTGTTCATGCACACCCAACATTGTCCGAGGTGCTGGACGAACTCTTTAAAGCAGCCAAG

upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
gtgagtccatgaactcatttgattcacagttgctgctgaacctttta-attcccagctaggatccttg-atttaccaatcaatattcgtcacgtcttgctatcgattgctgtgtattcctaaaacaactggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG
                                    |||   | | |      | | |||     | | ||||    ||   | |||    | |  |||||   |  ||| |  |||   | |  |||   |||| |         ||||||||||||||||||||||||| || || || || ||||||||| |||| || || |||||||| || |||
-----------------------------------gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgcta---aacgct-taaatttgcaca-taaccttttgtaccct----gcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG

upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
-----------gtgagtccatgaactcatttgattcacag----ttgctgctgaacctt--ttaattcccagctaggatccttgatttaccaatcaatattcgtcacgtctt----gctatcgattgctgtgtattcctaaaaca--actggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG
            |   |||||   | |||   |||  ||      |  | |  || | |  |||  ||   |  | ||| | | || |    |   |||    |||     |    | |     || |  |  |||| | |      ||     || |  | ||   ||||||| ||||||||||||||||| ||||| ||||| || || ||  | ||||| || |||||  | ||||||
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaaatcctctttacatctatggcatgattcattatgttttgactcataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctg--cagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG

upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 13
gtgagtccatgaactcatttgattcacagttgctgctgaaccttttaattcccagctaggatccttgatttaccaatcaatattcgtcacgtcttgctatcgattgctgtgtattcctaaaacaactggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG---------------------------
                                                                                  || |  | ||  |  | ||  |  |    | ||| |     |  ||||||      | |   |||| ||||||||||| || || || ||||||||| | || ||||||||||||||| | |||||| | || |||                           
---------------------------------------------------------------------------------gtttgctatgtgataat-tccctcacacactcttcttttcttacatggttg----aatcgtccagGAGATCAAGTTTGCCGTCCACGCGCATCCCACCCTCTCGGAAGTTTTGGACGAGTTATTCAAGTCGGCCAAGGTTCGCTGGCTTCAAGTTTTTGTTTAG

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|162239089|gb|FC416228.1|FC416228
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|67692532|gb|BJ952765.1|BJ952765
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|162195482|gb|FC370899.1|FC370899
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|162185502|gb|FC362571.1|FC362571
EST:     ACCTTATTCAGGAAGCCTCAAACGCTATTGCGATGGGCAACCCCTTCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATTTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|162167618|gb|FC343750.1|FC343750
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|7584064|gb|AW699962.1|AW699962
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|162170368|gb|FC346773.1|FC346773
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|67694918|gb|BJ955151.1|BJ955151
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|208380575|gb|DC919361.1|DC919361
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|162166908|gb|FC343293.1|FC343293
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|162239088|gb|FC416227.1|FC416227
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
EST: gi|15728076|gb|BI740607.1|BI740607
EST:     ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGG                         GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC
genomic: ACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGAC

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: 27 (upstream exon), 29 (downstream exon)
Score: 6

AGACACTGGCGAAATTCTGGGTGTTCACATTCTTGGTCTCCATGCCGCTGACCTTATTCACGAAGCCTCAAACGCTATTGCGATGGGCAACACCATCAGGgtgagtccat ... tcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgctatcgattgctgtgtattcctaaaacaactggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG
                       tcctaaa  putative branch site (score: 6)
                                      ttgttcttctt  putative PPT
                          taaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtccatgaactcatttgattcacagttgctgctgaaccttttaattcccagctaggatccttgatttaccaatcaatattcgtcacgtcttgctatcgattgctgtgtattcctaaaacaactggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT