Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA

Basic information

species Physcomitrella patens
transcript PP1S108_163V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
gtcaccaatatacgtggaaaaaacgat--gcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
 |  |  ||  |    ||   | |  |   |||  |   |  ||   |    |||   ||  ||  |  ||||  | | |   |||   || | |     ||| || ||||| ||||||||| | ||||| ||||||||||| ||||| || |||||||| || |||||||| || || ||||||||| | || || || ||
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgc-ttcttgtaaccggctcactttgatat-cttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: LOC_Os06g06350.2 (Oryza sativa), 3'ss of exon 10
gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacg-aatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
|| | |  | |   |  ||     |   ||   ||  | |    |||||   |          | ||||| | | |    |   ||  ||| || |  |||| ||| |||| ||||||||  || ||||   | |||| || |||||| | ||||| ||||| ||||||||||| |||||||||||| ||||||| |||||
gttagctgtttctat--aatctctgggacatgctagttgactataatggcattatttttttcagatgatg-actatatgccaaataccatgtataatacagGGGATGTTGGCGAGTGGCAACCAAATGGGTCCTTGAAAATCATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggag----agcgctgatgtattctgattcttttata---atgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
        | |     || |    |||  |  ||      |  ||||    || |        |   || | || |  | | |     |||   ||   |    |||| || ||||| ||||||||| | || || ||||||||||| |||||||| |||||||| || |||||||| || |||||||| ||  |||| || || ||
-------gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM5G812228_T01 (Zea mays), 3'ss of exon 10
gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
|| |   || | ||       |||   |  |    | |  | || |    || |     | || |     |||   ||  | || | ||||| ||       |||||||| ||||||||| |||||||   | | ||  | |||||  | ||||||||||||||||||||||| ||||| |||||  ||||||| |||||
gttagttatttccgcaacttcaacacagatgggggtattcatgagtttatcttggaataatcgtt--ctaattaaaatagtcttgtgatgcagGA-------GATATTGGCGAGTGGCAGCCAGATGGATCCTTAAAAGTGATTGATAGAAAGAAGAATATTTTCAAGCTTTCGCAGGGGGAATACGTTGCAGTGGAAAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 15
gtcacca-atatacgtggaaaaaacgatgcagtttatgtaaacgaat--ggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
|| |    || || ||     |||   ||  |||||| |      ||  | || |||    |  | |   | |  | | ||||    || ||  ||  | |||| |||||||||||||||||  |  |||| |||||||| |||||||| || ||||||||||| || |||||||| || ||||||||| |||| ||||||||
gttatttcatttatgttttccaaa-attgaggtttatattcttatattagctgttgggttgggtcacaattttccttttattcacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
gtcacca-atatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
|| |    || || ||     |||   ||  |||||| |      ||   ||||  ||    |  |  |   || | |||     || ||  ||  | |||| |||||||||||||||||  |  | || |||||||| |||||||| || ||||||||||| || |||||||| || ||||||||| |||| ||||||||
gttatttcatttatgttttccaaatt-tgaggtttatattcttatatta-gctgttgggtcacagttttccttttt-attaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
gtcaccaatatacgtggaaaaaacgatgcagtttatgt--aaacgaatggtgctg----gaggagagcgctgatgtattctgattcttttataatgcatg-aatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
                      |   | ||||||||||   ||  |    ||||     | |||  ||       |||| | |||| |  ||  |  ||  || |||| ||||||||||||||||   |  |||| | |||||| |||||||| || ||||||||||| || |||||||| || ||||||||| |||| || |||||
------------------gttcatttttcagtttatgtttgaataagatatgcttctacgtggattgcatgatcatatttt-attcatgaatggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA20G01060.1 (Glycine max), 3'ss of exon 15
gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
          ||     |        || | |  |  | |||  |  |   || |    | | |  |   ||||  || |     |||  |||    ||||||| |||||||| |||||  || ||||   |||||| |||||||| || ||||||||||| || ||  | ||||| |||||||||||||| || || ||
---------gtaaaaccaggttgtcctggattcaaaattaacatagtgatttgtaaatcaacacaaa---attcacatacag--gtaaaccattg--cagGTGACATTGGAGAATGGCAATCAAATGGGGCCATGAAAATTATTGATCGGAAGAAGAATATCTTTAAATTGTCTCAAGGAGAATATATTGCTGTGGAGAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
-----gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
          |  |  || || | | ||  |   ||  |||         | || |    || |||  ||  |   |||| |  || |  |  |       ||||||||| |||| ||||||||  ||||||| ||||||||||| |||||| | ||||||||||| || || || || || ||||| ||| |||| || || ||
gtatttctttctctgaacttgtatacaattagttagaatattggtttttgtagtcc----ggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
gtcaccaatatacgtggaaaa--aacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattc-ttttataatgcatga---atcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
|| || || |  |     |     |  ||   | ||   || |   |   |  |  |    ||  || || ||   |  ||  ||| |  |||  |     | |||||||| |||| ||||||||  || |||| ||||||||||| |||||||| || ||||| || ||||| ||  | || ||||| ||| | || || || ||
gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA

upper sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
-gtcaccaatatacgtggaaaaaacgatgcagttta-tgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaat---cagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
  |  |  ||||   ||| |       |  | || | | |  | |     |  |    |    || |  | ||  |    |   | || |   ||   |   |||| ||| |||| ||||||||  | ||||| |||||||| ||||| ||||| |||||||| || ||||||||||| || ||||||||  |||| || || ||
gtttgctcatat---tggcatttcttcttgaattaagttttgaggtcctctattttgtggattcgtttctttaa-caaccttgctgatgacttatcttttcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA

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: 33 (upstream exon), 33 (downstream exon)
Score: 11

CGAGGAGAGATATGCATTCGTGGAAAAACGGTATTTTCGGGATATTACAAACGCCCGGAACTCACGGAGGAGGTTCTTGTTGATGGTTGGTTTCACACAGgtacgccttg ... catgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
                          ttctgat  putative branch site (score: 11)
                             tgattcttttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - tgctgga