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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttctgtctccacttcgcgagcagcactgcgcctgaaaagcggctaagtggtttcagtttgttcgtggtctgtttctggcgatccatacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA

Basic information

species Physcomitrella patens
transcript PP1S452_4V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S452_4V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G046055_T01 (Zea mays), 3'ss of exon 1
----gcttctgtctccacttcgcgagcagcactgcgcctgaaaagcggctaagtggtttcagtttgttcgtggtc-tgtttctggcgatccatacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA
     |  | | | || ||||           | | || ||   ||   |    | | ||  ||   |||  ||  ||  ||    | | | | | |||  |||||| || ||  | || || || || ||  | || ||||||||||| || || || || ||||||||||||||||| ||| | |||||||||||| | ||||
gtaatcccccgacccctcttcctctcttcatgttcaccagatctgctcttgtccgatctcgtttgaatcgccgttgtgaatcgattgtttccttcgtttccgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGTATCGTGCCGCGCCACATCCAGCTGGCGGTGCGGAACGACGAGGAGCTGAGCA

upper sequence: PP1S452_4V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G54690.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------------------------------------------------gcttctgtctccacttcgcgagcagcactgcgcctgaaaagcggctaagtggtttcagtttgttcg------tggtctgtttctggcgatccatacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA
                                                                     | |  ||  | ||  |||     || |   ||   |    | |  |  |||   || | |||       || ||| ||    |   |  ||| | |  |  ||||| | ||  |||| |||||||| || ||||||||||||||||  || || ||||| || ||||| ||||| |||||||| ||||| || ||| | || |
gtaacaaacaatcttctgtttggtatttagtcttttagtctctatgatgagaatcactcgtaattgatatatcactagatttttcgatgtttaccgaatctttgattttgatttgatgttaaggtgtcttctagagtctgatctcttatatgatgttgatataatcat-tagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATCGTACCACGGCACATTCAGCTTGCAGTGAGGAACGATGAAGAGCTTAGTA

upper sequence: PP1S452_4V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv14s0030g00450.t01 (Vitis vinifera), 3'ss of exon 1
gcttctgtctccacttcgcgagcagcactgcgcctgaa-aagcggctaagtggtttcagtttgttcgtggtctgtttctggcgatcca----tacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA
     | |  | | || |    ||  |  ||    ||  |  ||| |    || |||  | | || |      |  || |  | |       |   ||    |||||  | ||  | || |||||||| || || || ||||| ||||||||||||||||| |||||||| ||||| ||||| || || ||||||||| ||||||
----ttttgacgaattggaacccaagaaagcataggattatacgggttttaggattcgctct-tttgaatcaagactcagatggtttgatggtgtgttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATTGTACCTCGCCACATACAGCTAGCAGTAAGGAATGACGAGGAGCTAAGCA

upper sequence: PP1S452_4V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ17602 (Selaginella moellendorffii), 3'ss of exon 1
gcttctgtctccacttcgcgagcagcactgcgcctgaaaagcggctaag-tggtttcagtttgttcgtggtctgtttctggcgatccatacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA
                               |   ||      ||| |  |  |||| ||    ||    |||   ||| | |||     |   |   |||||  | ||  | || ||||| |||||  | ||||||||||||||||| ||  | ||| | ||||||||||| || ||||| |||||||||||| | ||||
-------------------------------gtgagattctttgctcatctcttttccgtcgtctcaatctctcaatctcgggatttcgtcccattcccagGTGATCGAGCTCGCTGGAAACGCCGCGCGGGATAACAAGAAGAATCGGATCATCCCCAGGCACATCCAGCTCGCCGTGAGGAACGACGAGGAGCTCAGCA

upper sequence: PP1S452_4V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ29068 (Selaginella moellendorffii), 3'ss of exon 1
gcttctgtctccacttcgcgagcagcactgcgcctgaaaagcggctaagtggtttcagtttgttcgtggtctgtttctggcgatccatacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA
                 | |||   |  ||| | |      |   |  || || ||| | | |  ||     | ||  |    |||   ||||    |||||  | ||  | || ||||| |||||  | ||||||||||||||||| ||  | ||| | ||||||||||| || ||||| |||||||||||| | ||||
-----------------gtgagattctttgctcgtct----ctttttcgtcgtctcaatctctcagtctcgggatttcgttcgtcc---cattcc--cagGTGATCGAGCTCGCTGGAAACGCCGCGCGGGATAACAAGAAGAATCGGATCATCCCCAGGCACATCCAGCTCGCCGTGAGGAACGACGAGGAGCTCAGCA

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|7584267|gb|AW700163.1|AW700163
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|162234448|gb|FC409479.1|FC409479
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|19777747|gb|BQ039223.1|BQ039223
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|162210478|gb|FC386774.1|FC386774
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|18338910|gb|BJ170936.1|BJ170936
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|162276230|gb|FC452389.1|FC452389
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|67691870|gb|BJ952103.1|BJ952103
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|208350554|gb|DC926245.1|DC926245
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|208366183|gb|DC955284.1|DC955284
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|67508647|gb|BJ941508.1|BJ941508
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|162210479|gb|FC386775.1|FC386775
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
EST: gi|162234447|gb|FC409478.1|FC409478
EST:     CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAG                         GTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT
genomic: CTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATT

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: 22 (upstream exon), 35 (downstream exon)
Score: 8

AAGAATTGCTAGGTTTTTGAAGGCTGGTAAATACGCCGAACGTGTGGGAGCTGGTGCACCTGTCTACCTAGCCGCAGTGCTGGAATATTTAGCGGCCGAGgtgatcattc ... atttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtggtttcagtttgttcgtggtctgtttctggcgatccatacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA
                                         atacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttctgtctccacttcgcgagcagcactgcgcctgaaaagcggctaagtggtttcagtttgttcgtggtctgtttctggcgatccatacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG