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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC

Basic information

species Physcomitrella patens
transcript PP1S3195_1V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 5
gtacagtcatggctcctgatgtggg-tgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                  || |    |||  | ||||| |||           |||||||    || ||  |     |  | ||| | |  || |  | |||  ||   |   |   | | | |||||||||||   |||||||| || ||||||||||||||||| |||||  ||||| | ||||||||| |    ||| | ||    ||||||    |  | ||
------------------atataatctgtaattttttgacatagcctagcatatgcagtca---atttaatg-----gttagtgtagagctgacctatttaccaaccatttatttttttcctgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTCACTCCCCTGACTCTTCAGAGGAAGAGGGCGAGAATCGCCCAGAAGAAGCAAAGAATTGC

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 5
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgcttt-------cagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                            | |||| |    |       || || ||||   | |   | |           | || |  | |||  ||| || || |        ||| | |       |||||||||||  ||||||||| || ||||||||| | |||||||||||  | ||  | |||||||||||    ||| | ||   |||||||  | |  ||||
-------------------------caccatattatattgtctgcatgtttgt-cagttttcaagtcaaaatata------tcttccaggtagctttctgcttacctacctaatggtgttgttgtgttgcagGCAAGAAGGTGAGCAAGGCTCCTAAGATCCAGCGTCTTGTGACTCCCCTCACCCTCCAGAGGAAGCGTGCCAGAATCGCTGACAAGAAGAAGAGGATCGC

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgcttt-cagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                             || ||| |  ||   |    | |    || | | ||| |     | |  |     |      | | |   |       |||  ||| | |||| |||||||||||  |||||||||||| ||||||||| |||||||||| || |||||  | |||||||||||   |||| | ||   |||||||  | |  ||||
-------------------------ctctgtgttt-gttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 4
gtacagtcatggctcctgatgtgggtgtcgtat-tttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgcttt-cagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                |  | ||  |||  ||   | |    | ||| |  |    || | | | | |    | |  |      || |||    |      || ||  |||  ||  | |||  |||||||||||   ||||||||||| ||||||||  |||||||||| || |||||  | |||||||||||   |||| | ||   |||||||  | |  |  |
----------------tactctgcttgttatacgctggatgggtttcttgacaatgagccacagtttt----ctgaagt-----tttcgaaccacaacaagctaac--ctgtatgtttccttggcagGCAAGAAGGTCAGCAAGGCACCTAAGATCCAACGGCTTGTGACACCCTTGACCCTCCAGAGGAAGCGTGCTAGAATCGCTGACAAGAAGAAGAGGATAAC

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G054136_T09 (Zea mays), 3'ss of exon 5
gtacagtcatggctcctgatgtgggtgtcgtat-tttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgcttt-cagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                |  | ||  |||  |    | |    | ||| |  |    || | | | | |    | |  |   |||     |    |      || ||  |||  ||  | |||  |||||||||||   ||||||||||| ||||||||  |||||||||| || |||||  | |||||||||||   |||| | ||   |||||||  | |  |  |
----------------tactctgcttgttatgcgctggatgggtttcttgacaatgagccacagtttt----ctgaagtttttg-----aaccacaacaagctaac--ctgtatgtttccttggcagGCAAGAAGGTCAGCAAGGCACCTAAGATCCAACGGCTTGTGACACCCTTGACCCTCCAGAGGAAGCGTGCTAGAATCGCTGACAAGAAGAAGAGGATAAC

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcg-tgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                                    |  |       ||   | || |    ||  || |  |    |  ||  | |||       | |||| |  | || |         | |||||||||||   |||||||| || ||||||||||||||||||||||| |||||  | ||||||||| |   |||| | ||   |||||||  | |  ||||
------------------------------------gtaagaaaa--ttagattcacttaaagagata-attgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcg-tgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
            |     |   ||||     | || |               | || |    ||  || |  |    |  ||  | |||       | |||| |  | || |         | |||||||||||   |||||||| || ||||||||||||||||||||||| |||||  | ||||||||| |   |||| | ||   |||||||  | |  ||||
-----------acaaacaagaagggtaagaaaattag--------------attcacttaaagagata-attgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagc-gggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                             ||      |    |||        |  ||  | ||   | |   | |    | ||||    | | |    | ||   || ||  |   ||    |||||||| |    ||||| || || |||||||||||||||||||| || |||||| | ||||||||| |   |||| | ||   |||||||  |    | ||
-----------------------------gtgagacactgaacttgagaaatagtggtttctgaatcacacttgagaaataatgttttctgaaacttgtttcttctgtttggatttttga---cagGCAAGGAAGTTAGCAAAGCCCCTAAGATCCAGAGGCTTGTGACCCCATTGACTCTTCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAAAATTGC

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 5
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgcttt-cagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                    || |||||  || |||       ||  |   | | | |     ||||  |  |     |||| ||      ||   | |  |      |   || |||| |  |||| |||||| | || || || || || || |||||||| |||||||| ||||||||||| ||||||||    ||| | |||   |||||   | |  | ||
--------------------gttggtgttctaatttct-----tttttgatgggaaatatgatatgtttactga----cattatttactaaagatgtatgattggtcttatctgtgtgcctggcagGTAAGAAGTGCAGTAAAGCTCCCAAAATACAGAGGCTGGTGACTCCCTTGACTTTGCAAAGGAAGCGGGCAAGAATTGCAGAGAAGAAAAAGAGAATTGC

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 5
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                                       | | | |   |||  |  |   |  || |         |||   |  | ||  | | | |  || |||   |           ||||||||||| | |||||||| || |||||||||||||| || |||||   |||  ||||||| ||||||    |  | ||    ||||||  ||| |||  
-------------------------------------gtaagttcctcctcggaccttaaaccgtgcat--------ccaaactcactagt-gtcgtgtcgtgtcgtgaactcctaaaaaaccagGCAAGAAGCGCAGCAAGGCCCCCAAGATCCAGAGGCTGGTTACTCCGCGGACGCTGCAGAGAAAGCGCGACCGCATTGCCGAGAAGAAGAGGCGCGTCCA

upper sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ26393 (Selaginella moellendorffii), 3'ss of exon 5
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                                       | | | |   |||  |  |   |  || |   |      || |  ||    | | | | |  |||  ||    |     |   ||||||||||| | |||||||| || |||||||||||||| || |||||   |||  ||||||| ||||||  | |  | ||    ||||||  ||| |||  
-------------------------------------gtaagttcctcctcggaccttaaaccgtgca--tccaaactcactagtgt--cgtgtcgtgtcgtgaactcc---taaaaac---cagGCAAGAAGCGCAGCAAGGCCCCCAAGATCCAGAGGCTGGTTACTCCGCGGACGCTGCAGAGAAAGCGCGATCGCATTGCCGAGAAGAAGAGGCGCGTCCA

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|7647909|gb|AW738892.1|AW738892
EST:     TGTGAGGAAATACGTCAACACCTATCGTCGCAGCTTTGTATCGGCCACAG                         GCAAGAAGAGGAGCAATGCACCGAAGATCCATAGGCTTGTGACTCCTTTGA
genomic: TGTGAGGAAATACGTCAACACCTATCGTCGCAGCTTTGTATCGGCCACAGgtacagtcat ... gtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGA




















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), 35 (downstream exon)
Score: 297

AAGAGAGCCACCAAAATTCGCAAGCTCTTCAATCTCACCAAGGAGGATGATGTGAGGAAATACGTCAACACCTATCGTCGCAGCTTTGTATCGGCCACAGgtacagtcat ... gtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC
                            tactgac  putative branch site (score: 297)
                                              tgctttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG