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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatctcagtgtgcagctcattaatatactaaatacaagcagtcaaaaatctagaagtagtatggtgaattttataacatatacatgtggctgcatgcagTGTTTCTTGAGAAGCCTGAGGAGGAGGAAAAAAGAAATGCTGGAAAATTGGGTCCATCGGGTTTGGCCCTGCATTATGCTAATATCATCAATCAGATTGA

Basic information

species Physcomitrella patens
transcript PP1S54_228V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S54_228V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 8
---ccatctcagtgtgcagctcat--taatatact----aaatacaagcagtcaaaaatctagaagtagtatggtgaattttataacatatacatgtggctgcatgcagTGTTTCTTGAGAAGCCTGAGGAGGAGGAAAAAAGAAATGCTGGAAAATTGGGTCCATCGGGTTTGGCCCTGCATTATGCTAATATCATCAATCAGATTGA------
     || | | |||   | || |   || |  ||    || ||  |||| |  | ||| || |  |  | ||   |||  ||||  |  | | ||   ||   || | ||      | |||||   |  || |  |   ||  |   |    | |||||| ||| | ||  | ||  |||||||||| ||||||||||||||||||||      
gtataattttattgtcacgttcttcgcaaaaggcttcataattattagcattacataat-tatatttgttgtgac-aatgatatagaagct-cttgctactatctg-actgcagACAGTGAAGCGCCACAAGAACCAGCTAAACACCAC-AATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCAAATATCATCAATCAGATTGATACTCT

upper sequence: PP1S54_228V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 5
ccatctcagtgtgcagctcattaatatactaaatacaagcagtcaaaaatctagaa-gtagtatggtgaattttataacatatacatgtggctgcatgcagTGTTTCTTGAGAAGCCTGAGGAGGAGGAAAAAAGAAATGCTGGAAAATTGGGTCCATCGGGTTTGGCCCTGCATTATGCTAATATCATCAATCAGATTGA------
     ||      | |  || || |   ||  || |    | | |    |  |    ||  ||||  | ||| | |||  | |   | |     | | | |       |||  ||||  | ||    |  |||    ||  | ||   ||||| ||| | ||  | ||  |||||||||||||||||||||||||||||||      
--ggttcttgaccctgtacaatagtt--cttgatcctgtgatttagttcttgaccctgtgatatgtggcattgtctaaagtttctttcttttatcttactgcagACAGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGA---TTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT

upper sequence: PP1S54_228V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 8
-ccatctcagtgtgcagctcattaatatactaaatacaagcagtcaaaaatctagaagtagtatggtgaattttataacatatacatgtggctgcatgcagTGTTTCTTGAGAAGCCTGAGGAGGAGGAAAAAAGAAATGCTGGAAAATTGGGTCCATCGGGTTTGGCCCTGCATTATGCTAATATCATCAATCAGATTGA------
 || || | |   || |     || |||      |     ||  |   | | ||    |  | |         |  |   |||     |  |   ||||||       |||  |  |  ||||       ||| ||  |  | ||   ||||||||| | ||| | || ||||||||||| |||||||||| |||||||||      
tccttccccgaacgctgacatatattatgaccgttttcttca-ccggtactgtatttatgatttatcattgactgaagattatcaccctaacactatgcagA---CAGTGAAGAATCACAGGAACCTACCAAACGACGTAATAGA---TTGGGTCCAGCAGGTCTTGCACTGCATTATGCAAATATCATCAGTCAGATTGATACTCT

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), 20 (downstream exon)
Score: 2

GTCATGGAGCAACTAGTGGATATTGCAAATTATCTGTACCAAGAGATTCAAGAGAAGTTCGGACCATACGgtatatgttt ... ctgcatgcagTGTTTCTTGAGAAGCCTGAGGAGGAGGAAAAAAGAAATGCTGGAAAATTGGGTCCATCGGGTTTGGCCCTGCATTATGCTAATATCATCAATCAGATTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatctagaagtagtatggtgaattttataacatatacatgtggctgcatgcagTGTTTCTTGAGAAGCCTGAGGAGGAGGAAAAAAGAAATGCTGGAAAATTGGGTCCATCGGGTTTGGCCCTGCATTATGCTAATATCATCAATCAGATTGA
                          ttataac  putative branch site (score: 2)
                    tgaattttataacata  TA-rich tract