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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaagagttttcatgactttaaattctttagtaatccaagcaattgccgtgaactactttaggcggcatgttgaaaaggcttgtatgtgttatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAACGTAACACGACTTTTCAGCGAGTGCTGCAAACAGGCTCTGATTTCCAGA

Basic information

species Physcomitrella patens
transcript PP1S31_338V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA03G01880.1 (Glycine max), 3'ss of exon 5
caaagagttttcatgactttaaattctttagtaatc-caagcaattgccgtgaac-tactttaggcggcatgttgaaaaggcttgtatgtgttatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAACGTAACACGACTTTTCAGCGAGTGCTGCAAACAGGCTCTGATTTCCAGA
 ||     ||| ||   |     |   |  ||| |  |||  ||      || |  |   ||| || |  | |||     |      | ||  |  ||||||||||| || ||||| |||||||| ||| |||| ||||||||||| || ||| | ||  | || |||||  | || ||| |||| ||    || ||  |  
-aagacagttttatatatacgtgtgtgtgtgtatttacaataaaacagtctgtatgtgacttaagcagtttattgttggtggaaccttttgc-actttgcagGCTCGAATTGATTCGCACAACAAAATTTTGTATGCACGGCATGCGGATCAAAGGAATGCCACCTTTCAAAGGGTTCTGGAAACTGGAAGGGAATTTGATC

upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA07G08370.1 (Glycine max), 3'ss of exon 5
----caaagagttttcatgactttaaattctttagtaatccaagcaattgccgtgaactactttaggcggcatgttgaaaaggcttgtatgtgttatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAACGTAACACGACTTTTCAGCGAGTGCTGCAAACAGGCTCTGATTTCCAGA
     | |   || |  |   |||   |   ||   |||  ||   | |    ||   |   ||| || |  | ||      |      | ||  |  ||||||||||| || ||||| |||||||| ||| |||| || ||||||||||| ||| | ||  | || |||||  | || ||| |||| ||    || ||  |  
tttgaagatgattcttttttttttttgtatctttacaataaaacagacttgtatgggat---ttaagcagtttatttttggtggaaccttttgc-actttgcagGCTCGAATTGATTCGCACAACAAAATTTTGTATGCGCGGCATGCAGATCAAAGGAATGCCACCTTTCAAAGGGTTCTGGAAACTGGAAGGGAATTTGATC
















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|162169509|gb|FC346073.1|FC346073
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|37845778|gb|BJ603786.1|BJ603786
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|67726052|gb|BJ976311.1|BJ976311
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|37851742|gb|BJ609750.1|BJ609750
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|162223424|gb|FC400315.1|FC400315
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|162200332|gb|FC376643.1|FC376643
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|162223425|gb|FC400316.1|FC400316
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|37836464|gb|BJ594472.1|BJ594472
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|208382267|gb|DC919255.1|DC919255
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|37847958|gb|BJ605966.1|BJ605966
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|37842497|gb|BJ600505.1|BJ600505
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|162200333|gb|FC376644.1|FC376644
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|37846187|gb|BJ604195.1|BJ604195
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
EST: gi|67728119|gb|BJ978378.1|BJ978378
EST:     CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAG                         GCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA
genomic: CAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 9

CATCTCAGTAGACCTGAACACAATGGCCAGTGCTTTCAAGACTAGTGTAACAGGGTTGGAGAAAGAGCTAGCTGCACTTATTACGGAAAATCAGATCCAGgtacattcca ... tatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAACGTAACACGACTTTTCAGCGAGTGCTGCAAACAGGCTCTGATTTCCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgtgaactactttaggcggcatgttgaaaaggcttgtatgtgttatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAACGTAACACGACTTTTCAGCGAGTGCTGCAAACAGGCTCTGATTTCCAGA
         tacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaagagttttcatgactttaaattctttagtaatccaagcaattgccgtgaactactttaggcggcatgttgaaaaggcttgtatgtgttatgttgcagGCTCGTATCGATTCACACAACAAGATTCTGTACGCACGGCATGCAGACCAACGTAACACGACTTTTCAGCGAGTGCTGCAAACAGGCTCTGATTTCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa