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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggataggattactgttttacctagtgcccctagtcctgtgctcgagcattcaattggttaatattaattctttcacgtactgtcgtgcatttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGGCGCCTCCTAGCTGTTGCATCCAGTTACACATACGAGGAGGGTGATAAAC

Basic information

species Physcomitrella patens
transcript PP1S70_190V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S70_190V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os07g39950.1 (Oryza sativa), 3'ss of exon 7
tgggatag----gattactgttttacctagtgcccctagtcctgtgc------tcgagcattca-attggttaatattaattctttcacgtactgtcgtgcatttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGGCGCCTCCTAGCTGTTGCATCCAGTTACACATACGAGGAGGGTGATAAAC
 |  ||||    |   ||| ||||    ||   | ||| | || |        ||    ||||| ||  |      ||| ||||||    |    || |    ||  |||||   | ||||| ||  | ||  | ||||| || ||||| || || ||||| || || || |||||||||||||||||||| ||||||||||| || | ||
-gtaatagtcccgcgaactattttttgaag-atctctaattctctattctgtatcacaaattcacatcagaatgccttagttcttttttttttcatcttttggtt--gcagTTTCCCAGATACCCATCCAGCATCGCTGCTCTGTCTTTCAGTAGGGATGGCCGTCTGCTTGCTGTTGCATCCAGTTACACTTACGAGGAGGGAGACATAC

upper sequence: PP1S70_190V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA20G26960.1 (Glycine max), 3'ss of exon 7
tgggataggattactgttttacctagtgcccctagtcctgtgctcgagcattcaattggttaatattaattctttcacgtactgtcgtgcatttat---gcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGGCGCCTCCTAGCTGTTGCATCCAGTTACACATACGAGGAGGGTGATAAAC
          ||  | |||    |  |||    |||  ||  |  ||   ||||  |||| ||| | ||||  |  |  | | ||  |  || | |    |||||||||| |||||| || ||  |||||||||| || |||||||||||||| |||||| | ||||||||||| |||||||||| ||| || ||   |||| 
---------gtttttatttcgtttt-tgcattgagtagtg-accagaattttcatatggtaaat-tcaattgcta-atttgccgttttctatctctctttcagTACTCAAAATATCCTACCAGCATTGCTGCACTGTCGTTTAGCAGAGATGGACGCCTCTTGGCTGTTGCATCAAGTTACACATTCGAAGAAGGGCCTAAAG

upper sequence: PP1S70_190V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA20G26890.1 (Glycine max), 3'ss of exon 7
tgggataggattactgttttacctagtgcccctagtcctgtgctcgagcattcaattggttaatattaattctttcac-gtactgtcgtgcatttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGGCGCCTCCTAGCTGTTGCATCCAGTTACACATACGAGGAGGGTGATAAAC
                                                                ||  ||||  | ||   | ||  ||    |  |  ||||||||| |||||| ||||| ||||| ||||| || |||||||||||||| |||||  | ||||||||||| |||||||||| ||| || ||   |||| 
-------------------------------------------------------------gtaatcgattcggttactaaattgctgttttctcttctagTACTCAAAATATCCAACTAGCGTTGCAGCACTTTCGTTTAGCAGAGATGGACGCCTGTTGGCTGTTGCATCAAGTTACACATTCGAAGATGGACCTAAAA

upper sequence: PP1S70_190V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA10G40440.1 (Glycine max), 3'ss of exon 7
tgggataggattactgttttacctagtgcccctagtcctgtgctcgagcattcaattggttaatattaattctttcac-gtactgtcgtgcatttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGGCGCCTCCTAGCTGTTGCATCCAGTTACACATACGAGGAGGGTGATAAAC
       |  ||| |  |||      |  |   | |   |||   ||   |||  |  | |||||   ||||  | ||   | ||  ||    |  |  |||| |||| |||||| ||||| ||||| || || || |||||||||||||| |||||  | ||||||||||| |||||||||| ||| |||||   |||| 
-------gttttattcctttttgcttttgcttaatttgagtgacagaattttct-taaggtaatac--attcggttactaaattgctgttttctcttctagTATTCAAAATATCCAACTAGCGTTGCAGCTCTTTCGTTTAGCAGAGATGGACGCCTGTTGGCTGTTGCATCAAGTTACACATTCGAAGAGGGACCTAAAA

upper sequence: PP1S70_190V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv03s0091g00710.t01 (Vitis vinifera), 3'ss of exon 7
tgggataggattactgttttacctagtgcccctagtcctgtgctcgagcattcaattggttaatattaattct---ttcacgtactgtcgtgcatttat---gcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGGCGCCTCCTAGCTGTTGCATCCAGTTACACATACGAGGAGGGTGATAAAC
               ||        |||   | | |  | |  || |   |||||||||  || | | | | |   |  |  | |||   ||||||| |    ||||| |||| ||| ||  | |||||||| |||||||| ||||||||||| || |||||  | ||||| ||||| ||||||||||  || ||||| || ||||
---------------gtaaacaactgtggaacaaattgtatcttctaat-ttcaattggagaaaagtgagtataactataatttctgctatgcatttgtcttccagTATTCAAAATACCCTTCAAGTGTTGCAGCACTATCGTTTAGCAGAGACGGTCGCCTGTTGGCTGTGGCATCAAGTTACACATTTGAAGAGGGAGACAAAC

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|162278201|gb|FC454436.1|FC454436
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|208382641|gb|DC923241.1|DC923241
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|208353625|gb|DC946363.1|DC946363
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|208354143|gb|DC957391.1|DC957391
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|162157028|gb|FC333390.1|FC333390
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|67725122|gb|BJ975381.1|BJ975381
EST:     TGGGTTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: TGGG-TTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|37847796|gb|BJ605804.1|BJ605804
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|18339928|gb|BJ171956.1|BJ171956
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|162278202|gb|FC454437.1|FC454437
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCT
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCT
EST: gi|67726764|gb|BJ977023.1|BJ977023
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAN                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|208367368|gb|DC951286.1|DC951286
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|162193204|gb|FC369964.1|FC369964
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|37826959|gb|BJ584971.1|BJ584971
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
EST: gi|37827919|gb|BJ585931.1|BJ585931
EST:     ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAG                         TACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG
genomic: ATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGG

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: 30 (upstream exon), 31 (downstream exon)
Score: 5

CTATGGCACGTTCGCAACAGGCGGTTGCGATGGGTTTGTCAATGTTTGGGACGGTAATAACAAGAAGCGCCTATATCAGgtatttcacg ... atttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGGCGCCTCCTAGCTGTTGCATCCAGTTACACATACGAGGAGGGTGATAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcattcaattggttaatattaattctttcacgtactgtcgtgcatttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGGCGCCTCCTAGCTGTTGCATCCAGTTACACATACGAGGAGGGTGATAAAC
                  tattaat  putative branch site (score: 5)
        aattggttaatattaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggataggattactgttttacctagtgcccctagtcctgtgctcgagcattcaattggttaatattaattctttcacgtactgtcgtgcatttatgcagTACTCAAGATATCCGACTAGTGTTGCTGCACTATCTTTTAGCAGAGATGGGCGCCTCCTAGCTGTTGCATCCAGTTACACATACGAGGAGGGTGATAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG