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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGATCAAAGCTATTCAGACTCGTTATCAGGGCGATCAAGAACGCATTCAATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgcttcgataagccctttctgtggagacacttgcattgtttggagagtaacttcaggttgttttgtgacatagaatatagtcgcagaggcacgctaatactaacttggtgctacacgaaactcgctaagaaacgttgtggtttctgattgtacag

Basic information

species Physcomitrella patens
transcript PP1S198_153V6.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S198_153V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 4
AAGATCAAAGCTATTCAGACTCGTTATCAGGGCGATCAAGAACGCATTCAATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgcttcgataagccctttctgtggagacacttgcattgtttggagagtaacttcaggttgttttgtgacatagaatatagtcgcagaggcacgctaatactaacttggtgctacacgaaactcgctaagaaacgttgtggtttctgattgtacag
                                       ||| | || ||  | || || ||  |||| |||||||| ||||||||||||||||| |||||| || || ||||       || |||| | |     | |   |   || || |||         |||||   |  |||      |  | | |   |   | || |  | | ||| |  ||                                          
---------------------------------------GAAAGGATACAGCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAGgt-cgcttacttc------tccattctttag-----cctat-taactttgatagt-----tgaattgttccattgcat----cttttttgtatgagtttgttatttattagttgatcatatt----------------------------------------
















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|162196338|gb|FC375408.1|FC375408
EST:     ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAG                         GGTGTCTGCCCACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
EST: gi|162158690|gb|FC335057.1|FC335057
EST:     ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAG                         GGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
EST: gi|162280189|gb|FC455998.1|FC455998
EST:     ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAG                         GGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
EST: gi|162186044|gb|FC361872.1|FC361872
EST:     ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAG                         GGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
EST: gi|162167977|gb|FC344291.1|FC344291
EST:     ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAG                         GGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
EST: gi|162184111|gb|FC358857.1|FC358857
EST:     CCCTCTTGCAG                         GGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: CCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
EST: gi|162198368|gb|FC373162.1|FC373162
EST:     ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAG                         GGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
EST: gi|162188717|gb|FC364003.1|FC364003
EST:     ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAG                         GGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
EST: gi|162160268|gb|FC336554.1|FC336554
EST:     ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAG                         GGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
EST: gi|162167655|gb|FC344281.1|FC344281
EST:     ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAG                         GGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG
genomic: ATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgc ... gattgtacagGGTGTCTGCCAACCCTTGCCACTTTACCGGTGTGGATTGGTCTGTATCGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATCAAAGCTATTCAGACTCGTTATCAGGGCGATCAAGAACGCATTCAATTGGAAACAGCAAGGTTGTACAAGCAGGCTGGAGTCAACCCTCTTGCAGgtgcggttgcttcgataagccctttctgtggagacacttgcattgtttggagagtaacttcaggttgttttgtgacatagaatatagtcgcagaggcacgctaatactaacttggtgctacacgaaactcgctaagaaacgttgtggtttctgattgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA