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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtcaaaagcaaaaccaaacccccagcgtcatgcgtcttttcgtttacattcttgtccgctttctccaactggatacgatttgcttttgtcgcgtattggtcgaaataacctgataatttgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG

Basic information

species Physcomitrella patens
transcript PP1S77_89V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 4
gttggtcaaaagcaaaaccaaacccccagcgtcatgcgtcttttcgtttacattcttgtccgctttctccaactggatacgatttgcttttgtcgcgtattggtcgaaataacctgataatttgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG
                                                                       ||| | ||   |||  |||| |     | |  |  | ||      ||      | |  | |   ||   |||     ||||     | | ||| ||        ||||||| || || ||| |||| ||||||||||| || ||||||||||| ||||| ||||| ||||   ||||||   |||||   |||   ||||| ||||
---------------------------------------------------------------------ggactaggtaatttttatttttatttaaaactactaaatatgttaatatcgcacacatcacaagcagg---caa-----ctttaggatactcttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 12
gttggtcaaaagcaaaaccaaacccccagcgtcatgcgtcttttcgtttacattcttgtccgctttctccaactggatacgatttgcttttgtcgcgtattgg--tcgaaataacctgataatttgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaat-agGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG
                                                                      || |||| |  | |||  | |  | |  | |||  | |     | |||||| |||| | |   |||  |||  |  | || |||    ||||||   |||  |   | |||||||||| || ||| ||||||||||||| ||||| |||||||| || ||||| || ||||||| | |||||| | |||||  ||||  |||||||||||
--------------------------------------------------------------------gtaagtggaaat-acttgtatgttccactgaatggggttgtttccaactgata-tttgttat---attttgtt--aggcattatttgcatcattttcctttatttacttcagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGCCCAACAAAACACATGCCAACACCTGAGCAATGGACTAATATTTTCAATCCAG

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
gttggtcaaaagcaaaaccaaacccccagcgtcatgcgtcttttcgtttacattcttgtccgctttctccaactggatacgatttgcttttgtcgcgtattggtcgaaataacctgataatttgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG
                                                            | |    || ||    | |    ||  |||| |    ||   || |||    || || |   |  | | ||| |    |    |  |  |||| | || |||||          ||||||||||| || ||| ||||||||||||| ||||| |||||||| |||||||| || |||||||   |||| | | |||||  ||||   ||||||||||
------------------------------------------------------------cacaaagtcaaagaaaaaagccattatttttctaaaata--agttgaa----ccagacatactcttattccagtactgtatggtattaatttctt-cacttttt----------tagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 13
gttggtcaaaagcaaaaccaaacccccagcgtcatgcgtcttttcgtttacattcttgtccgctttctccaactggatacgatttgcttttgtcgcgtattggtcgaaataacctgataatttgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG
                                                            | |      ||     | |  |||    ||| ||    ||  |  |||    || || | | |  | |  || |    |    |  |  ||   | || |||||          ||||||||||| || ||| |||| |||||||| ||||| |||||||| |||||||| || |||||||   |||||| | |||||  ||||  ||||||||| |
------------------------------------------------------------cacaaagctcagaaaaaaataatta---tttttctaaaataagctgaa----ccagacattatcttatttcagtactgtatggtattaattctctacacttttt----------tagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 12
gttggtcaaaagcaaaaccaaacccccagcgtcatgcgtcttttcgtttacattcttgtccgctttctccaactggatacgatttgcttttgtcgcgtattggtcgaaataacctgataatttgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG
                                                         ||  || |||   | ||  | |  |  |    |   |  || ||   |  |||||   | |  ||||  |        |||| |  ||  |  ||     ||||              ||||||||||||| ||| |||| |||||||| ||||| |||||||| || || || || |||||||   | || ||  |||||  |||  | |||||||| |
---------------------------------------------------------gttagcattcat-atcttcaaataacctctaatccgcatgtcttta-cacaataaagagttggtttgact--------ggttgctgtctcttgtttgc-tatttc-------------agGTTGTTGGATTTGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGTCCCACAAAACACATGCCCACTCCAGCTCAATGGACTAACGCATTCAATCCTG

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|162268981|gb|FC445473.1|FC445473
EST:     TTTCTGTGGATCCCTCCTCTCATCCACAGCTTCATGTCTTACTCTCGATG                         GTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCA
genomic: TTTCTGTGGATCCCTCCTCTCATCCACAGCTTCATGTCTTACTCTCGATGgttggtcaaa ... aaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCA




















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), 25 (downstream exon)
Score: 2

GCAGTCTTTTGAGACAATCCTGGAAAATGTGTTCGCTCCTCTGTTCGAGGTTTCTGTGGATCCCTCCTCTCATCCACAGCTTCATGTCTTACTCTCGATGgttggtcaaa ... aaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG
                                   attttttgttaaatga  TA-rich tract