Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggtgtagagctgaatttaggcttggcgaaggtcgaagtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG

Basic information

species Physcomitrella patens
transcript PP1S131_131V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os04g55970.2 (Oryza sativa), 3'ss of exon 2
gggtgtag-agctgaatttaggcttggcgaaggtcgaagtggttgagggtcatgtcctggtctgaggatgttgg--ggggtgtattgtgtgtttgatt---tgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
     ||| ||  |  |||    ||   |   || ||||      | |  ||  |  | ||     ||| ||     |||  ||     |  ||| ||   | ||||||||| ||||| ||| |||||||||| ||||||||||| || |  ||  |    || || || |  ||||| || || ||||
-----tagtagtagttttttttgttaatgggagtagaagaatcaaatgacca-atatttgttcagagattttaattagggcataaaaaatccttggttatgtatagGCATCGGTGGACCGGAAGGTACGAGGCGCATCTGTGGGATAACAGCTGCCGGCGTGAGGGCCAGAGCCGCAAGGGACGCCAAG

upper sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G086573_T01 (Zea mays), 3'ss of exon 2
----gggtgtagagctgaatttaggcttggcgaaggtcgaagtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtt-tgatttgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
         ||      | |  ||      |  |  |   | |  ||  ||||  ||||   |||| |  || || || | |||  | | | |  |||||| |||||| || ||||||||  ||||||||||||||||||||||||| |  ||  ||   ||||| || |  ||||| || || ||||
agaaaaaaataacaagcagtcaagctgcaccatatatt--attaattacgggttttgtct--gtctaaa-atcttaggtgatgtggtatttttggtgatttctagGCACCGGTGGACTGGCAGGTACGAGGCACATCTGTGGGACAACAGCTGCCGACGCGAAGGGCAGAGCCGCAAGGGCCGCCAAG

upper sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G399072_T02 (Zea mays), 3'ss of exon 2
-----------------------------gggtgtagagctgaatttaggcttggcgaaggtcgaagtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
                               | | |    ||  |  | |||  |       | | || |||    |   ||  |     |   ||||   | | |||| |     | |  || || |||||  | ||||| || ||||||||||| || ||||||||||| ||||| || |||||||| || ||| | |||||  | ||||
gttggccttagttgatgtgctgcgcgcatcagcgcatgcatgcgtacatgctcaggatctcgcaacgtcgttcctagct-tgatcgatcgtcctgatgcgtgcgtgtgtctaaatggatctatctgcagGCACAGATGGACCGGGCGGTACGAGGCTCACCTGTGGGACAACACTTGCAGGAAGGAAGGCCAGACTAGGAAAGGGAGGCAAG

upper sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G399072_T03 (Zea mays), 3'ss of exon 2
-----------------------------gggtgtagagctgaatttaggcttggcgaaggtcgaagtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG-----------------
                               | | |    ||  |  | |||  |       | | || |||    |   ||  |     |   ||||   | | |||| |     | |  || || |||||  | ||||| || ||||||||||| || ||||||||||| ||||| || |||||||| || ||| | |||||  | ||||                 
gttggccttagttgatgtgctgcgcgcatcagcgcatgcatgcgtacatgctcaggatctcgcaacgtcgttcctagct-tgatcgatcgtcctgatgcgtgcgtgtgtctaaatggatctatctgcagGCACAGATGGACCGGGCGGTACGAGGCTCACCTGTGGGACAACACTTGCAGGAAGGAAGGCCAGACTAGGAAAGGGAGGCAAGGTGAGTGAGAGCTTAGC

upper sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA16G00950.1 (Glycine max), 3'ss of exon 4
-----gggtg-tagagctgaatttaggcttg---gcgaaggtcg--aagtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttga-----------tttgt-agGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
     | ||  | ||  | ||| |    ||       ||  ||   |  | ||| ||     |||  |  | ||| ||  || |    | | || |   ||||            ||||| |||||| | ||||||||| | || ||||| ||| ||||||| |||| ||| ||||||||||| |||||  | |||||  | ||||
gttaggagtaatggattttaatgttaatttttttaaaaaaatcatcacatagtttagtactttgtt-tattttgatgaactttgcttctttttttttcttttggggttcatggattttgttagGCATAGATGGACTGGAAGATATGAGGCCCATTTGTGGGATAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG

upper sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G04260.1 (Glycine max), 3'ss of exon 3
----gggtg-tagagctgaatttaggcttggcgaaggtcgaagtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgt------ttgattt--gtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
    | ||  ||||  | ||| |    ||    |  || | | ||||| || |   |||     |    | || |||     | |  | |  ||      | |||||   ||||||| | ||||||||  | || ||||| ||| |||||||||||| ||| ||||||||||| |||||  | |||||  | ||||
gtaggagtaatagattttaatgttttttt--taattgttgca-tggtttagtgctttgtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG

upper sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 2
gggtgtagagctgaatttaggcttggcgaaggtcga-agtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttgattt-gtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
                        |     | |||| |    ||||  |  || |   ||          | |   |    ||   | |||||||   | |||||||| ||||||||||| ||||||||||||||||||||||||| |||| ||||||| || || ||  | |||||  | ||||
------------------------gtacgtgatcgacaacttttgatcgatatatggagg-----aaccatagctagactaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG

upper sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 2
gggtgtagagctgaatttaggcttggcgaaggtcga-agtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttgattt-gtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
                        |     | |||| |    ||||  |  || |   ||          | |   |    ||   | |||||||   | |||||||| ||||||||||| ||||||||||||||||||||||||| |||| ||||||| || || ||  | |||||  | ||||
------------------------gtacgtgatcgacaacttttgatcgatatatagagg-----aaccatagctagtctaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG

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|18356869|gb|BJ188928.1|BJ188928
EST:     TCCATCGATACCTTCGGCCAGAGAACATCTGTGTACAGAGGCGTCACTAG                         GCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAG
genomic: TCCATCGATACCTTCGGCCAGAGAACATCTGTGTACAGAGGCGTCACTAGgtgggtgtcc ... tgatttgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAG
EST: gi|18346002|gb|BJ178045.1|BJ178045
EST:     TCCATCGATACCTTCGGCCAGAGAACATCTGTGTACAGAGGCGTCACTAG                         GCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAG
genomic: TCCATCGATACCTTCGGCCAGAGAACATCTGTGTACAGAGGCGTCACTAGgtgggtgtcc ... tgatttgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAG

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), 30 (downstream exon)
Score: 4

GCAAGCGAGGCGCCGGGCGGTCTGACAACAAAGATCCGTCCCCCCGCAAGTCCATCGATACCTTCGGCCAGAGAACATCTGTGTACAGAGGCGTCACTAGgtgggtgtcc ... tgatttgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
                                          gtttgat  putative branch site (score: 4)
                                           tttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggtgtagagctgaatttaggcttggcgaaggtcgaagtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG