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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGTGCTTACCCTGCCAAGTCCCTCTCCCGGTTTGCCGACATCGTTGCCTTGTGTGTCCAGgtaacgagttttctcacatgtagtcacctgcttgtatgatatcataatacccagtcagatagtaggggacaaccacctttggatcaaattcatactgctaatcatgataaattcattagttatatattattttaattctaatacaccttccatgtggtatttgtggacag

Basic information

species Physcomitrella patens
transcript PP1S64_28V6.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S64_28V6.2 (Physcomitrella patens), 5'ss of exon 16
lower sequence: LOC_Os03g08550.2 (Oryza sativa), 5'ss of exon 14
TATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGTGCTTACCCTGCCAAGTCCCTCTCCCGGTTTGCCGACATCGTTGCCTTGTGTGTCCAGgtaacgagttttctcacatgtagtcacctgcttgtatgatatcataatacccagtcagatagtaggggacaacca---cctttggatcaaattcatactgctaatcatgataaattcattagttatatattattttaattctaatacaccttccatgtggtatttgtggacag
 || |||||| | |  |||||||| ||||| ||| |  |||||   |||||||||||||| |||||||||||||||||| |  | || |||||||||||||||  |  |||   ||      |         | |   |||  | | |||| | | | || | |  | |   |     | | || | |||||||||  | |                                                                        
CATCGATGCATTGGACAGAATGGTCGATCCTGCGCTGAAGGGTCTGTACCCTGCCAAGTCTCTCTCCCGGTTTGCCGACGTGCTCGCTTTGTGTGTCCAGgta--ggatttcaccatcctatgcagatgagctatgcaatacta-attacctaat-acatggaacagaatgtctgaatcttatgaaacaaattcatgttacag----------------------------------------------------------------------

upper sequence: PP1S64_28V6.2 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GRMZM2G071573_T01 (Zea mays), 5'ss of exon 15
TATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGTGCTTACCCTGCCAAGTCCCTCTCCCGGTTTGCCGACATCGTTGCCTTGTGTGTCCAGgtaacga-gttttctcacatgtagtcacctgcttgtatgatatcataatacccagtcagatagtaggggacaaccacctttggatcaaattcatactgctaatcatgataaattcattagttatatattattttaattctaatacaccttccatgtggtatttgtggacag
 || |||   ||||| |  ||||| ||||| ||  | || ||    ||||||||||||||||||||||| || ||||||||  | ||| | || |||||||||  |  | |    || ||| || ||    ||  |  ||  ||            || | ||    |  |   ||    ||||  ||  |     |  |  |                                                                    
CATCGATCTGCTCGCCAAGATGGTCGATCCTGCACTGGATGGGCTGTACCCTGCCAAGTCCCTCTCCCGTTTCGCCGACATAATCGCCATCTGCGTCCAGgtactgttggtgctgcatatgcag-cataaactcctccgaactctcttcttttttgcaaagagccttgttctttcagaggtggactaagatggccttcttttttgcag---------------------------------------------------------------

upper sequence: PP1S64_28V6.2 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GRMZM2G162531_T03 (Zea mays), 5'ss of exon 12
TATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGTGCTTACCCTGCCAAGTCCCTCTCCCGGTTTGCCGACATCGTTGCCTTGTGTGTCCAGgta---acgagttttctcacatgtagtcacctgcttgtatgatatcataatacccagtcagatagtaggggacaaccacctttggatcaaattcatactgctaatcatgataaattcattagttatatattattttaattctaatacaccttccatgtggtatttgtggacag
 || |||   ||||| || ||||| ||||| ||| | || ||    |||||| |||||||||||||||| || ||||||||| | ||| | || |||||||||   ||| |  ||||     |   | | ||||    |    |||   ||  |   |    | | |    |        |||   |    ||  |  |  |   ||                                                                  
CATCGATCTCCTCGCCAGGATGGTCGATCCGGCGCTGGACGGGCTGTACCCTTCCAAGTCCCTCTCCCGTTTCGCCGACATCATCGCCATCTGCGTCCAGgtacgtacgcgcgttctttgccgctat-agctgcacaaagtccatctcgatctcttct---gtgggaaaaaaggcttgtttttttgttttttttttttttttttgcag-----------------------------------------------------------------

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|162151051|gb|FC326868.1|FC326868
EST:     CTGCCAAGTCCCTCTCCCGGTTTGCCGACATCGTTGCCTTGTGTGTCCAG                         CCCGAACCCGAATTCCGACCTCCTATATCTGAAGTAGTGCAGTCCCTGGTA
genomic: CTGCCAAGTCCCTCTCCCGGTTTGCCGACATCGTTGCCTTGTGTGTCCAGgtaacgagtt ... ttgtggacagCCCGAACCCGAATTCCGACCTCCTATATCTGAAGTAGTGCAGTCCCTGGTA
EST: gi|162151050|gb|FC326867.1|FC326867
EST:     GTTTGCCGACATCGTTGCCTTGTGTGTCCAG                         CCCGAACCCGAATTCCGACCTCCTATATCTGAAGTAGTGCAGTCCCTGGTA
genomic: GTTTGCCGACATCGTTGCCTTGTGTGTCCAGgtaacgagtt ... ttgtggacagCCCGAACCCGAATTCCGACCTCCTATATCTGAAGTAGTGCAGTCCCTGGTA
EST: gi|162155001|gb|FC331419.1|FC331419
EST:     CTGCCAAGTCCCTCTCCCGGTTTGCCGACATCGTTGCCTTGTGTGTCCAG                         CCCGAACCCGAATTCCGACCTCCTATATCTGAAGTAGTGCAGTCCCTGGTA
genomic: CTGCCAAGTCCCTCTCCCGGTTTGCCGACATCGTTGCCTTGTGTGTCCAGgtaacgagtt ... ttgtggacagCCCGAACCCGAATTCCGACCTCCTATATCTGAAGTAGTGCAGTCCCTGGTA

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: 18 (upstream exon), 18 (downstream exon)
Score: 1

TATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGTGCTTACCCTGCCAAGTCCCTCTCCCGGTTTGCCGACATCGTTGCCTTGTGTGTCCAGgtaacgagtt ... ttgtggacagCCCGAACCCGAATTCCGACCTCCTATATCTGAAGTAGTGCAGTCCCTGGTAAGGCTTATGCAGCGTGCAGCTTTAAGTAAACGCCGGCATGAGTACAACG




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