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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagatgcaagtcatttgctgaggtggtcattttctctactcaacatcttattacttttatgattggatccctaagcttcttttttgttgtattggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA

Basic information

species Physcomitrella patens
transcript PP1S50_118V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S50_118V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g08760.1 (Oryza sativa), 3'ss of exon 3
cagatgcaagtcatttgctgag-gtggtcattttctctactcaacatcttattacttttatgat-tggatcccta--agcttcttttttgttgtattggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA
  ||||   || |||    ||  | |  || || ||    |||  ||  | ||| | || || | |  ||  ||     |||    | | || |||     ||||| |||||||| || ||||  || || || ||||||||||||||||| || |||||||||||| |||| ||||| || || |     || ||| || |  
--gatgttggtaattcttggaatgggagcaattgcttaggtca-tattctgttaatattttgctgtaaataactgctgtcttgggatctcttttatcctt-cagGACTACGAGTATGCGAGTTTTAATCCTGTGGCATTTGACATTGCTAATCACTTCTGTGAGATGTCTGCTGATTATCATTCAGCCACACCTCATGTGCTGG

upper sequence: PP1S50_118V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G425249_T01 (Zea mays), 3'ss of exon 3
----cagatgcaagtcatttgctgaggtggtcattttctctactcaacatcttattacttttatgattggatccctaagcttcttttttgttgtattggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA
      ||  | | |  | ||   || |    ||  |||||  |||  |  || || |||     |                 | | || |  | |||   |||||||| ||||| || || | |||||| || |||| |||||||||||||||||||||||||||| | || || || || ||     |||| ||| |  |  
gttttggagactactactatgtgaagata--tatgctctctgttcataaagtttttgcttcgt--accaacctttcgtaacagtgtcttctctttttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG

upper sequence: PP1S50_118V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G087146_T01 (Zea mays), 3'ss of exon 3
--cagatgcaagtcatttgctgaggtggtcattttctctactcaacatcttattacttttatgattggatccctaagcttcttttttgttgtattgga-gcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA
   |  ||  || | |  |  ||| |  |  | | |   |    | | | | ||| |  | | | |  || ||   || |  ||  | || ||||    |||||| || || || || ||||  ||||| || ||||| ||||||||||| || |||||||||||| |||| ||||||||  |       || ||| ||||  
acaacttgacagacctgcgaggagttcttgttctaccaaatcttagaccatgttattcctgtaacttaatgcc---gccttgttgatcttttattctctgcagGACTATGAATATGCGAGTTTTAACCCAGTCGCATTCGACATTGCTAATCACTTCTGTGAGATGGCTGCTGATTACCATACATCAACACCACATGTGTTGG

upper sequence: PP1S50_118V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G74320.1 (Arabidopsis thaliana), 3'ss of exon 4
--cagatgcaagtcatttgctgaggtggtcattttctctactcaacatcttattacttttatgattggatcc-----ctaagcttctt-ttttgttgtattggag-cagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA
   || |   |   ||||| | ||   |   |  | | | |     ||   ||||||   |  | |||||||     || |  || || ||||||  |||   |   ||||||| || ||  |  | || || || || || | ||||||||| || || |||||||||||| |||||||||||||| ||||    || ||  |  |  
gtaaggtttcatgaatttgtttagtcagctctccttttttc---gtataccattactagaaaaaatggatcctaactctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG

upper sequence: PP1S50_118V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ23622 (Selaginella moellendorffii), 3'ss of exon 3
cagatgcaagtcatttgctgaggtggtcattttctctactcaacatcttattacttttatgattggatccctaagcttcttttttgttgtattggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA
         ||   || ||     || | ||||   |  |  |  |||| || || || |  || | |  || |   |  ||   ||||      | ||||| |||||||||||||| ||||| ||||| || ||||||||||| || || ||||| |||||| |||||||||| ||| | ||    || ||   | |  
---------gtgcgtttctttcaaggcctttttgcttggtgga--tcttctttctcttct--ttagttttctcaatctaattaacgttggtgcttaacagGACTACGAGTACGCCAGCTACAATCCCGTGGCGTTTGACATTGCGAATCACTTCTGCGAGATGGCTGCCGATTATCACACGGAATCTCCCCACCGGCTGG

upper sequence: PP1S50_118V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ05852 (Selaginella moellendorffii), 3'ss of exon 3
cagatgcaagtcatttgctgaggtggtcattttctctactcaacatcttattacttttatgattggatccctaagcttcttttttgttgtattggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA
         ||   || ||     || | ||||   |  |  |  |||| || || ||    || | |  || |   |  ||   ||||      | ||||| |||||||||||||| ||||| ||||| || ||||||||||| || || ||||| |||||| |||||||||| ||| | ||    || ||     |  
---------gtgcgtttctttcaaggcctttttgcttggtgga--tcttctttctcttcc--ttagttttctcaatctaattaacgttggtgcttaacagGACTACGAGTACGCCAGCTACAATCCCGTGGCGTTTGACATTGCGAATCACTTCTGCGAGATGGCTGCCGATTATCACACGGAATCTCCCCACCGCCTGG

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|37850877|gb|BJ608885.1|BJ608885
EST:     AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATA                         GATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
genomic: AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATAgtacgtgctt ... attggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
EST: gi|67695099|gb|BJ955332.1|BJ955332
EST:     CAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATA                         GATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
genomic: CAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATAgtacgtgctt ... attggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
EST: gi|208386046|gb|DC956562.1|DC956562
EST:     AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATA                         GATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
genomic: AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATAgtacgtgctt ... attggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
EST: gi|162272172|gb|FC448681.1|FC448681
EST:     AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATA                         GATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
genomic: AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATAgtacgtgctt ... attggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
EST: gi|162170654|gb|FC347150.1|FC347150
EST:     AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATA                         GATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
genomic: AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATAgtacgtgctt ... attggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
EST: gi|208395668|gb|DC920258.1|DC920258
EST:     AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATA                         GATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT
genomic: AATATGGCAATATCATGGTTTCAGAGAAAGATGACTCCGTCACACTCATAgtacgtgctt ... attggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttattacttttatgattggatccctaagcttcttttttgttgtattggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA
     ttacttttatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagatgcaagtcatttgctgaggtggtcattttctctactcaacatcttattacttttatgattggatccctaagcttcttttttgttgtattggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG