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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTTGATGAAACTGAACAATGAGACGGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttcaaagttagtatggcgtctttttcttaccctaattctacatcacggtgaggtaggtctgagacatattcgatttcgcccttatttaataat...

Basic information

species Physcomitrella patens
transcript PP1S37_118V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_118V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 5'ss of exon 2
ATTTTTGATGAAACTGAACAATGAGACGGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttcaaagttagtatggcgtctttttcttaccctaattctacatcacggtgaggta----ggtctgaga-catattcgatttcgcccttatttaataat
 || |||||||| |||||||| ||||||||| |||| ||||||||||| || ||||  || || || || ||||| |||| |   ||   |  |   |    | ||||| ||    |  ||||   |  ||| | | ||    ||| || || |    ||  | | | |  | |        
GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGGCACCACCGTCCATGGCACCATCACTGgtacgatgtcttggcgaccttt---tttttttgttgttgttgttctttttggcggcgcgttactagggtttgcgagcggcgtctgtgttgtctatgtggcgcg--

upper sequence: PP1S37_118V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ29766 (Selaginella moellendorffii), 5'ss of exon 2
ATTTTTGATGAAACTGAACAATGAGACGGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttcaaagttagtat--ggcgtctttttcttaccctaattctacatcacggtgaggtaggtctgagacatattcgatttcgcccttatttaataat
|||| ||||||| || ||||| ||||| ||||| || |||||||||||||| || |||||| | || || ||||||||| ||   || | | |||| |   |||  | |||  |    ||| | | | |     |  |||  ||                                   
ATTTCTGATGAAGCTAAACAACGAGACAGTATCCATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAGgtttgatctctaggctagtttctagcgattgttttctctgataagtttccctttttctctggtgtgtag---------------------------------

upper sequence: PP1S37_118V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ08912 (Selaginella moellendorffii), 5'ss of exon 2
ATTTTTGATGAAACTGAACAATGAGACGGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatg-tgt-tcaaagttagtat--ggcgtctttttcttaccctaattctacatcacggtgaggtaggtctgagacatattcgatttcgcccttatttaataat
|||| ||||||| || ||||| |||||||||||||| |||||||||||||| || |||||| | || || ||||||||| || ||| || | | |||| |   |||  | |||  |    ||| | | | |     |  |||  ||                                   
ATTTCTGATGAAGCTAAACAACGAGACGGTATCGATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAGgtgtgatgtctctaggctagtttctagcgattgttttctctgataagtttcccttttcctctggtgtgtag---------------------------------

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|162210344|gb|FC386224.1|FC386224
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|208364908|gb|DC947050.1|DC947050
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|18345230|gb|BJ177271.1|BJ177271
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|162217222|gb|FC391962.1|FC391962
EST:     TATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: TATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|208375129|gb|DC956469.1|DC956469
EST:     GGTATNGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GNGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|208369557|gb|DC932539.1|DC932539
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|162217223|gb|FC391963.1|FC391963
EST:     TATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: TATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|208388874|gb|DC932902.1|DC932902
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTTGATGAAACTGAACAATGAGACGGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttcaaagttagtatggcgtctttttcttaccctaattctacatcacggtgaggtaggtctgagacatattcgatttcgcccttatttaataat

- - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - AGCTCA