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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgttagtcatgctcaaaatatttgatggctcttggcctttcacaacgtgctttgtttcctttggcattgcatttcagggtattcaattgcctttcttctttgtgcgggggagcaaacctacacacgtgtattgtttgacgcagtttttcctacactgtag

Basic information

species Physcomitrella patens
transcript PP1S452_30V6.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgttagtcatgctcaaaatatttgatggctcttggcctttcacaacgtgctttgtttcctttggcattgcatttcagggtattcaattgcctttcttctttgtgcgggggagcaaacctacacacgtgtattgtttgacgcagtttttcctacactgtag
 ||  ||||||| ||||||||||| ||||| || || || || ||||| |||||||||||  || | |||||||| ||||  ||||| ||||| ||||||||| || ||  |     ||||   |   | ||    | |   |||    ||    | |     ||||  |||||     | |   || |   |    |     |                                                       
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgttat-ttggttttattgattctgttttcagttgttgtaactcatttgagcttc----acattttatttctaca-acttggttccaggttgggtacactcca-----------------------------------------------------

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 13
GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgttagtcatgctcaaaatatttgatggctcttggcct--ttcacaacgtgctttgtttcctttggcattgcatttcagggtatt-caattgcctttctt--ctttgtgcgggggagcaaacctacac-acgtgtattgtttgacgcagtttttcc---tacactgtag-------------------------------
 || || ||||| ||||| || ||||| ||||| || || || ||||| |||||||||||| |  | |||||||| ||||||||||| ||||| ||||||||      |  |  |  |||   ||    ||     |  ||||     | ||||  | | | |    ||  |||      ||||   ||  ||| |      |||    ||       ||   |||   | | | |||  |   ||| |||        | | ||| |                               
TGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTCTGATATACTCTAAGCAGgtagaagcttgtttatgtatcaaataatactgatttttgttcatctgattcttttgtgcttctcttgttaaattctttaatattgttatgacctatagaggttttaattggcctgtataattaacattgcatatcttgcctt-tgcattttactggaacaaattgtggctgatcattttcattactttttccgctacag

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 13
GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgtt-agtcatgctca---aaatatttgatggctcttggcct--ttcacaacgtgctttgtttcctttggcattgcatttcagggtatt-caattgcctttcttctttgtgcgggggagcaaacctacacacgtgtattgtttgacgcagtttttcctacactgtag
 ||||| ||||| ||||| || ||||| ||||| || || || ||||| |||||||||||| |  | |||||||| |||||||| || ||||| ||||||||  || | || | |   |  |||   ||    ||     |  ||||  |  |  |||  | | | |    ||  |||      ||||   ||  ||| |                                                                  
TGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTCTAATATACTCTAAGCAGgtagaggcttgtttatttatgtatcaaataatactgatttttgttcatcagattgttttgtgcttctcttgttaaattctttaatattgttatgacctat------------------------------------------------------------------

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 13
GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgttagtcatgctcaaaatatttgatggctcttggcctttc---acaacgtgctttgtttcctttggcattgcatttcagggt-attcaattgcctttcttctttgtgcgggggagcaaacctacacacgtgtattgtttgacgcagtttttcctacactgtag
 || |||||||| |  || || ||||| || ||||| || || |||||||| ||||||||| || | || ||||| ||||||||||| ||||| |||||||| | | |  |  ||  | |||  | |   ||    ||     ||||      | ||     |  |  ||  ||||  |  | |||  ||   ||      ||| ||      || | |  |    |  |||||| |||  |      |||  |   ||| ||
CGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTCTGATATACTCAAAGCAGgt-aatgaaac--aatttttttattaggcttttattttatagaacaataaaaatagtggtactatgagttatattttggtctcattacataatctaatcattttttgttttatagtagatgt---taaatgtattttttccc------ttttatttgctgaag

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 13
GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgttagtcatgctcaaaatatttgatggctcttggcctttcacaacgtgctttgtttcctttggcattgcatttcagggtat--tcaat----tgcctttcttctttgtgcgggggagcaaacctacacacgtgtattgtttgacgcagtttttcctacactgtag
 || ||||||||||| || || || || || ||||| || || |||||||||||||| ||| || | || ||||||||||| ||||| || || ||||||||   |  || |  |  |   |     |          |      ||| ||   |   |||    |||  |||     ||   ||| |    ||| ||  ||  || | |   |  | |                                              
TGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCCTGATATATTCTAAGCAGgt--attttgttttagtttagtagaatcataaaaatgctggtgttgtgattaaatgtttttaaatttgttttttttaatactatcagtctgatgcattcttttcttttcctttgatgaag---------------------------------------------

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 13
GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgt-----tagtcatgctcaa-aatatttgatggctcttggcctt-tcacaacgtgcttt-------gtttcctttggcattgcatttcagggtattcaattgcctttcttctttgtgcgggggagcaaacctacacacgtgtattgtttgacgcagtttttcctacactgtag
 || ||||||||||| || || || || || ||||| || || |||||||||||||| ||| || | || ||||||||||| ||||| || || ||||||||     |  ||  | | |  |  ||   |    | ||||  || | |  |  || |||       ||||  |||   | |   |||| |  |||    ||  ||||    ||  ||  |                                                     
TGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCCTGATATATTCTAAGCAGgtattttttttctagtttagtagaatcataaaaatattggtgttgtgattaaatgtttttaaattagttttttttaatactatctttctga-tatattcttttcttttcctttgatgaag-----------------------------------------------------

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 13
GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgttagt--catgctcaaaatatttgatggctcttggcctttcacaacgtgctttgtttcctttggcattgcatttcagg----gtattcaattgcctttcttctttgtgcgggggagcaaacctac-acacgtgtattgtttgac-gcagtttttcctacactgtag
 ||  | ||||| || || || || || || || || || || |||||||| ||||||||||| || |||||||| || |||||||| ||||| |||||||| | |  |||| || |  | || | || |||||   |    |  |  || ||| |||| |||  |  |  | ||         | |   | | | ||| || |  ||           |    |  |   |  | | |  | || |   ||| | |  | ||||||
TGCACTCAAAATATATATTAAAGCGAGAGCAACTCCGAAAGTTGTTGCAGCCTTTGCTGAGCGTCGGGAGTTTGACAAAATTCTGATATACTCAAAGCAGgtgaatagcatgatctaggttttcgttgcctcttaaacaa--aatatatgttttttttctttttcctgtaaaatttgtttcttatctgttactactttttttatcagtaatattttattattgaattatgggcatttagagtaactgtgttttcttcgtcgctgtag

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 13
GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgttagtcatgctcaaaatatttgatggctcttggcctttcacaacgtgctttgtttcctttggcattgc-atttcagggta-ttcaattgcctttcttctttgtgcgggggagcaaacctac-acacgtgtattgtttgacgcagttt-ttcctacactgtag------------------------------------
 ||  ||||||| || || || || ||||| || || || || |||||||| ||||||||| || | ||||| ||||| ||||| || ||||||||||||||   |     |   | | ||| |     ||    ||||   |   |  ||| | ||       ||| | |  |||  ||| ||        ||      || |   |   |    |  ||| |    ||   |  |        ||| || |||  || |                                      
TGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTCTAATATACTCCAAGCAGgtatatatattttgtattctttcaattacctaaatctttttaagattattttctgtcaaaatctattactaaatcatagtagtttgggaattttatcatattatatagcacaatgcatatactatctatgcccttatcattattttttattgctattctttgaatggtctttgtacttctgattttttcatctatgcag

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: 31 (upstream exon), 32 (downstream exon)
Score: 6

GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgttagtcatg ... tacactgtagGTTGGGTATACACCAGATTATCTGTTCCTGCTGCAGACAATACTGCTATCAGATCCTCAG




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