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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAGTGGTAGGAATTATCGAGGAGGCTTTGAAACGGCCGTCATGTTCAAAGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgttctaacctttctcttgaaaattttctggtttttagagttttatgatcggagctattagaagctcaatggagttactagttttgtcaccgttagtgacatctaccgtgctcctttgcag

Basic information

species Physcomitrella patens
transcript PP1S61_267V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os11g20790.1 (Oryza sativa), 5'ss of exon 3
CTTAGTGGTAGGAATTATCGAGGAGGCTTTGAAACGGCCGTCATGTTCAAAGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgttctaacctttctcttgaaaattttctggtttttagagttttatgatcggagctat-tagaagctcaatggagt-tactagttttgtcaccgttagtgacatctaccgtgctcctttgcag
||| || || |||||||| || || ||  ||||    || ||||||  ||||||||| ||||||||||| ||||| || || ||||| || |||||||||| ||     || ||    || | || | | ||  | |    | | | | || |  |    || || |||        || | |  |||  ||   |    |||  | | || |  | |  ||        
CTTGGTTGTTGGAATTATTGATGAAGCCATGAAGAAACCTTCATGTCAAAAGGGTTTCATTCTTGATGGGTTCCCACGGACAGTTGTTCAGGCACAGAAGgtattcgatttgta---cttttattaatagtt--cagccaataaaaatatttttctttaggcaatgtagctatgttttgaactacactgtttactttcgggttcataatatttttcttcttcag------

upper sequence: PP1S61_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os12g13380.1 (Oryza sativa), 5'ss of exon 3
CTTAGTGGTAGGAATTATCGAGGAGGCTTTGAAACGGCCGTCATGTTCAAAGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgttc-taacctttctcttgaaaattttctggtttttagagttttatgatcggagctattagaagctcaatggagttactagttttgtcaccgt-tagtgacatctaccgtgctcctttgcag
||| || || || ||||| || || ||  ||||     | |||||    || |||||||| |||||||| |||||  | |||||||| |||||||||||||   |    ||  | |   | | |    | ||      | |  |    |||| | ||  ||||| |    |  | ||||||    |   || | |||  || |         |||          |||||
CTTGGTTGTTGGGATTATTGATGAAGCCATGAAGAAAACTTCATGCCAGAAAGGTTTTATCCTTGATGGTTTCCCTAGAACTGTTGTTCAAGCACAGAAGgtgaggtccttggtcaatatgcaccgctatataaaagagctcct----ttttgttattagagctgtctata--taaatgga----cagtttctatcattgtatcacttttcttactaaaaaatggtgcag
















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|208384519|gb|DC914991.1|DC914991
EST:     AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|37850614|gb|BJ608622.1|BJ608622
EST:     GTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: GTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|208373590|gb|DC952415.1|DC952415
EST:     TCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: TCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|18369302|gb|BJ201388.1|BJ201388
EST:     AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAG
genomic: AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAG
EST: gi|7147997|gb|AW509919.1|AW509919
EST:     AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|208363576|gb|DC939767.1|DC939767
EST:     AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|208357429|gb|DC910742.1|DC910742
EST:     AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|162152017|gb|FC328438.1|FC328438
EST:     TTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: TTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|162152018|gb|FC328439.1|FC328439
EST:     AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|162258565|gb|FC434780.1|FC434780
EST:     AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|162258566|gb|FC434781.1|FC434781
EST:     AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAG                         TTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
genomic: AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAAC
EST: gi|100431663|gb|BY960311.1|BY960311
EST:     AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGGAG                         TTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAA
genomic: AGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTT-GGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAA

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: 33 (upstream exon), 32 (downstream exon)
Score: 13

CTTAGTGGTAGGAATTATCGAGGAGGCTTTGAAACGGCCGTCATGTTCAAAGGGTTTTATTCTTGATGGCTTCCCCCGCACTGTTGTCCAAGCACAGAAGgcatgaatgt ... tcctttgcagTTGGATGCCGCTCTTGAGAAGCAAGGCGTAAAGGTTGACAAGGTTCTGAACTTTGAGATTGAAGATTCTGTCCTTGAAGAGCGTATTACTGGGCGGTGGA




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