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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataattaggtttggcatctttttgttaaagtggttgttatgaacacatacaaagatgtggtgaacaaattggtggaacgttggtttt...

Basic information

species Physcomitrella patens
transcript PP1S46_324V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os05g30800.1 (Oryza sativa), 5'ss of exon 3
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataatt-aggtttggcatctttttgttaaagtggttgttatgaac--acatacaaagatgtggtgaacaaattggtgga-acgttggtttt
 ||||| |||||||| || ||||||||||| ||||| || |||||||||||| | || || || || ||||||||||| |||||    | |||  ||| || ||   |    ||||     | ||  |  |  | | |       ||  ||||  || |      ||| ||    || ||  || |
GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgt----ttggtgcatatttcagacattttttcttcagtatgaaaggaatcctgtaacttggtttaacaagagatgattcctgtatttgtcattacattttttat

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os01g16190.1 (Oryza sativa), 5'ss of exon 3
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataattaggtttggcatctttttgttaaagtggttgttatgaacacatacaa-agatgtggtgaacaaat-tggtggaacgt-tggtttt
|||||| ||||||||||||||||| || || ||||| || ||||| || ||| | || || || |||||||| |||||||||||    || | ||||  |    |||   |  ||||  | ||||  |   || |   |||||   | | |||     ||   || ||    ||| | |||    
ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtg-catatgcttattctacctttttataagttttgttaaaaggagcaattgttt-cacatttgacaaatggaaacaattgatgtgtccaaacatgtggcac-

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G467059_T03 (Zea mays), 5'ss of exon 3
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatt-taggtttataattaggtttggcatctttttgttaaagt-ggttgttatgaacacatacaaagatgtggtgaacaaattggtg-gaacgttggtttt
 ||||| ||||| || |||||||| || || ||||| || || ||||||||| | || ||||| ||||||||||||||||||||  ||  |  |  |    |      || | |  | | | ||| | || |    |       | ||  |   |      ||  |   |   ||   || |   
GCCAGAAATGGTTGTAGGCTGGTATCACTCACATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaaatccacttgtttaaaagggaccggtctatgaaaataggatagcttctgttgttgcactgtactatatgtcatgtcattataaatactgat---

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA15G09410.1 (Glycine max), 5'ss of exon 3
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgt--aatttaggtttataattaggtttggcatctttttgttaaagtggttgttatgaacacat-acaaagatgtggtgaacaaattggtggaacgttggtttt-
|||||||||||| || |||||||||||||| ||||| || ||||| || ||| | ||||| || || |||||||| ||||||||  || ||   ||  |  ||   |||      ||| | |     |   |||  |||||  ||  | || |||   | ||    ||| ||     ||||||   
ACCAGAGATGGTTGTTGGCTGGTACCATTCGCATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttcatttctttctt---tttaattgttttctttgttgattcctgtgttgaacctattgctaatatggctttaattgtttgctgcctt-ttggttaat

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv18s0001g10820.t01 (Vitis vinifera), 5'ss of exon 3
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataattaggtttggcatctttttgt----taaagtggttgttatgaacacatacaaagatgtggtgaacaaattggtggaacgttggtttt
||| ||||||||||| || ||||||||||| ||||| || ||||| |||||| | ||||| ||||| || || || || |||||   |     |  | ||    | || |||  | | ||        ||  || |||| |  |     |    |    |  | ||    ||   | ||  |    
ACCTGAGATGGTGGTAGGATGGTACCATTCACATCCTGGATTTGGCTGCTGGCTCTCTGGTGTGGACATTAACACACAACAGgttggtccttatcttcatcctttgtgacattatgtagtgctcctgtgtaattattattattattattattattactattgataagcaagtaagaagtaag----

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EDP09161 (Chlamydomonas reinhardtii), 5'ss of exon 4
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataattaggtttggcatctttt----tgttaaagtggttgttatgaaca-catacaaagatgtggtgaacaaattggtggaacgttggtttt
 || ||||||||||||||||||||||| || || || || || || |||||| |||| |||||||||||||| || ||||||||   ||    |        |    || |||  |      |  |   |    ||   |  || | ||    |  | || |   | |   |   | ||   |    
CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtcgtgcgggggcgtgcaggaatcgctcaagccgcaagtctccccgtagcgtgcagcgtaagctggcggggcgcg-acaccaggcaaccgcacg----

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ33925 (Selaginella moellendorffii), 5'ss of exon 3
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataattaggtttggcatctt-tttgttaaagtggttgttatgaacacatacaaagatgtggtgaacaaattggtggaacgttggtttt
    || ||||| || || ||||||||||||||||| |||||||| |||||| | || || || || ||||| || ||||| ||||       |   | ||| ||||  | | || ||||||    |  |  || |   ||                                          
GAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAAgtaagaatctatagaacttaagtttcacgttttctttgtttgctttttcttttttgtcag-----------------------------------------

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ37436 (Selaginella moellendorffii), 5'ss of exon 3
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataattaggtttggcatctttttgttaaagtggttgttatgaacacatacaaagatgtggtgaacaaattggtggaacgttggtttt
    || ||||| || || ||||||||||||||||| |||||||| |||||| | || || || || ||||| || ||||| ||||       |   | ||| ||||  | | || ||  |       || || |   ||                                          
GAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAAgtaagaatctatagaacttaagtttcacgttttctttgtttgccttttctttttgtcag-----------------------------------------

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|67573473|gb|BJ946297.1|BJ946297
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|67692976|gb|BJ953209.1|BJ953209
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208388020|gb|DC933140.1|DC933140
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCANCAN                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTANCANTANTANTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|162224586|gb|FC400482.1|FC400482
EST:     CGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTNTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: CGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208384664|gb|DC915239.1|DC915239
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|162173753|gb|FC349929.1|FC349929
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGGTAGCAGTAATAGTGGATCCAAT
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGG-TAGCAGTAGTAGTGGATCCAAT
EST: gi|208390625|gb|DC937557.1|DC937557
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208378926|gb|DC922772.1|DC922772
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208400245|gb|DC908906.1|DC908906
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|162224587|gb|FC400483.1|FC400483
EST:     GGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: GGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208378125|gb|DC902598.1|DC902598
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|22131888|gb|BQ826859.1|BQ826859
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208395571|gb|DC928986.1|DC928986
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208368927|gb|DC947485.1|DC947485
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|18329512|gb|BJ161518.1|BJ161518
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCA
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCA
EST: gi|208362822|gb|DC950622.1|DC950622
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|162150910|gb|FC327390.1|FC327390
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|67696853|gb|BJ957086.1|BJ957086
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|67569711|gb|BJ942535.1|BJ942535
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208387484|gb|DC933347.1|DC933347
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208369314|gb|DC955859.1|DC955859
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|100420708|gb|BY993475.1|BY993475
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|162150909|gb|FC327389.1|FC327389
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|18335934|gb|BJ167955.1|BJ167955
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
EST: gi|208364180|gb|DC947284.1|DC947284
EST:     ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC
genomic: ATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATC

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: 29 (upstream exon), 32 (downstream exon)
Score: 7

ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttagg ... ggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATCCAAAGTGTGAAAGGAAAGGTTGTGATCGATGCTTTTCGATTGATCAACC




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