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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAAGAAGGCGTTGCCTGCTAATGCCAAGATTGCCAAAGATGCGAAGGAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccatttgatatggtttttcggtgtcatatgtcgcatgttgcccttgtcttactgtttctttacgtccgctaatgtggccgttggaccgtaataacg...

Basic information

species Physcomitrella patens
transcript PP1S25_89V6.2
intron # 2
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S25_89V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA10G33550.2 (Glycine max), 5'ss of exon 2
TCATGAAGAAGGCGTTGCCTGCTAATGCCAAGATTGCCAAAGATGCGAAGGAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgt-atccatttgatatggtttttcggtgtcatatgtcgcatgt----tgcccttgtcttactgtttctttacgtccgctaatgtg--gccgttggaccgtaataacg--------------------------------------------------------------------------
|||||||||||||  ||||| | |||| ||||||||| || ||||| || || ||| | ||||| || ||||| ||||||||||| ||||| || ||||||| |  || ||  ||     | |   | ||   |     || |    ||   ||   ||  |   ||   | ||    ||||||   || |  |     ||||                                                                              
TCATGAAGAAGGCTCTGCCTCCCAATGGCAAGATTGCGAAGGATGCAAAAGACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcag

upper sequence: PP1S25_89V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT2G37060.3 (Arabidopsis thaliana), 5'ss of exon 2
TCATGAAGAAGGCGTTGCCTGCTAATGCCAAGATTGCCAAAGATGCGAAGGAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccatttgatatggtttttcggtgtcatatgtcgcatgttgcccttgtcttactgtttctttacgtccgctaatgtggccgttggaccgtaataacg--------
||||||| |  |   | ||||||||||  || || || |||||||| |||||||  || || || ||||| || ||||||||||||||| |||| |||||||||   |||  ||    ||||     |  ||||| |  | |||| |||| || | |||||     |      | ||  |  | |||     || |  |         
TCATGAAAAGAGGTCTTCCTGCTAATGGGAAAATCGCTAAAGATGCTAAGGAGATTGTGCAGGAATGTGTCTCTGAATTCATCAGTTTCGTCACCAGCGAgtatgtctttttta-accttttaacaatgctatgttgtgt-ttgctcttg-ctgaatgtttagaggc-----ttgataggaactttgagttttagtttcaagtcttaa

upper sequence: PP1S25_89V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
TCATGAAGAAGGCGTTGCCTGCTAATGCCAAGATTGCCAAAGATGCGAAGGAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccat-ttgatatggtttttcggtgtcatatgtcgcatgttgcccttgtcttactgtttctttacgtccgctaatgtggccgttggaccgtaataacg
||||||||||||||||||| |||||||  ||||| ||||| ||||||||||| || || |||||||| || ||||| ||||||||||||||||| ||||||||  |   |   | |   |||||  |  | | | |  | |       |||| ||   | || |||   |      |||    | ||      || |    
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttc-tccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc

upper sequence: PP1S25_89V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv06s0004g03490.t01 (Vitis vinifera), 5'ss of exon 1
TCATGAAGAAGGCGTTGCCTGCTAATGCCAAGATTGCCAAAGATGCGAAGGAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccatttgatatggtttttcggtgtcatatgtcgcatgttgcccttgtcttactgtttctttacgtccgctaatgtggccgttggaccgtaataacg-----
|||||||||||||  | || || || | |||||| ||||| ||||||||||||||  | ||||| || |||||||| ||||||||||||||||| |||||||||      | | | ||||||   ||||   || || |  ||| |   || |    | |     |  |  |  || ||    |  | |    ||    |     
TCATGAAGAAGGCTCTTCCGGCCAACGGCAAGATCGCCAAGGATGCGAAGGAGACTCTCCAAGAATGCGTTTCCGAGTTCATCAGTTTCATCACCAGCGAgtatgag---ggttttgtttttaattgtcg-gtgccgtaatttggctccgtttggtcgctgagaaaattttggaaaagttaa-gaggaattaaaactttgaattt

upper sequence: PP1S25_89V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ15374 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCGTTGCCTGCTAATGCCAAGATTGCCAAAGATGCGAAGGAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccatttgatatggtttttcggtgtcatatgtcgcatgttgcccttgtcttactgtttctttacgtccgctaatgtggccgttggaccgtaataacg
| |||||||||||| |||| || ||||| ||||| ||||| ||||| |||||||| || ||||| || || || || |||||||| |||||||| ||||||||   ||| | |  | |  || |  || || |     || || |   |   ||   |                                          
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCGGAGTTCATCAGCTTCATCACTAGCGAgtaagtatt-gcttcgatcctttgtggtgatgttaactatctt-cttctactttgtag------------------------------------------

upper sequence: PP1S25_89V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ24973 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCGTTGCCTGCTAATGCCAAGATTGCCAAAGATGCGAAGGAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccatt-tgatatggtttttcggtgtcatatgtcgcatgttgcccttgtcttactgtttctttacgtccgctaatgtggccgttggaccgtaataacg
| |||||||||||| |||| || ||||| ||||| ||||| ||||| |||||||| || ||||| || || || || |||||||| |||||||| ||||||||   |||     | | | ||||| |    | ||  | ||  |  | || |  |||| |                                         
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCAGAGTTCATCAGCTTCATCACTAGCGAgtaagtattgctggaagttctttcgatcctttgtggtg-atactatc-ttcttctactttgcag-------------------------------------

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|67697971|gb|BJ958204.1|BJ958204
EST:     GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGA                         AGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
genomic: GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccattt ... cctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
EST: gi|162273472|gb|FC449617.1|FC449617
EST:     GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGA                         AGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
genomic: GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccattt ... cctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
EST: gi|208354191|gb|DC957411.1|DC957411
EST:     GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGA                         AGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
genomic: GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccattt ... cctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
EST: gi|208361426|gb|DC935113.1|DC935113
EST:     GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGA                         AGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
genomic: GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccattt ... cctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
EST: gi|162273471|gb|FC449616.1|FC449616
EST:     CAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGA                         AGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
genomic: CAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccattt ... cctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
EST: gi|37828975|gb|BJ586987.1|BJ586987
EST:     TCATCAGTTTCATCACGAGCGA                         AGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
genomic: TCATCAGTTTCATCACGAGCGAgtatccattt ... cctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
EST: gi|208387454|gb|DC949239.1|DC949239
EST:     GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGA                         AGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA
genomic: GAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccattt ... cctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGA

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), 31 (downstream exon)
Score: 8

TCATGAAGAAGGCGTTGCCTGCTAATGCCAAGATTGCCAAAGATGCGAAGGAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccattt ... cctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGATTTACTTTGGGCCATGAGCACATTAGGGTTTGAAGACTACGTCGAGCCG




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