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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctcatgtttgacatgtagattttttttccaaaccatttgtgaataggtcatagttcaccaagagctcagaatgtagacttttgcttttgtcacattggttatacaattgctgacttctgggatgatgtctgtatcctctgttttatag

Basic information

species Physcomitrella patens
transcript PP1S62_157V6.4
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_157V6.2 (Physcomitrella patens), 5'ss of exon 11
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
GGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctcatgtttgacatgtagattttttttccaaaccatttgtgaataggtcatagttcaccaagagctcagaatgtagacttttgcttttgtcacattggttatacaat--tgctgacttctgggatgatgtctgtatcctctgttttatag----------------
 ||||| |||||||| || ||| | || |||||||| |||||||||||||| |||||  |||| || ||||| ||||| || || ||| | || || ||||| | ||  |      |  | | ||   | |||       ||     | |       | || |   |    | |     |  ||  ||  |  ||  |         ||   |  || | || | |||  | || | | | | |     || ||                  
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggatttta---aactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag

upper sequence: PP1S62_157V6.2 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
GGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctcatgtttgacatgtagattttttttccaaaccatttgt-gaataggtcatagttcaccaagagctcagaatgtagacttttgcttttgtcacattggttatacaattgctgacttctgggatgatgtctgtatcctctgttttatag
 || || ||||||||||||||| | || || ||||| || ||||||||||| |||||| ||||||||||||| || || || |||||| | |||||||||||||       |||  |    |  |          | ||   | ||  ||||                                                                                                       
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaatat--gagttgaatgcttcaacacacaactaacacagctagtcaaatacag----------------------------------------------------------------------------------------------------

upper sequence: PP1S62_157V6.2 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
GGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctcatgtttgacatgtagattttttttccaaaccatttgt-gaataggtcatagttcaccaagagctcagaatgtagacttttgcttttgtcacattggttatacaattgctgacttctgggatgatgtctgtatcctctgttttatag
 || || ||||||||||||||| | || || ||||| || ||||||||||| |||||| ||||||||||||| || || || |||||| | |||||||||||||       |||  |    |  |          | ||   | ||  ||||                                                                                                       
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatat--gagttgaatgcttcaacacacaactaacacagctagtcaaatacag----------------------------------------------------------------------------------------------------

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|162203496|gb|FC380412.1|FC380412
EST:     ATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAG                         GACTCTTCAGTAATTGCTCAATTAGGCTGGCCAGACATGCGGCTTCCCATC
genomic: ATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctca ... tgttttatagGACTCTTCAGTAATTGCTCAATTAGGCTGGCCAGACATGCGGCTTCCCATC
EST: gi|162272850|gb|FC448006.1|FC448006
EST:     TGTTGTCCATCCCC-ATNCAATCATTCATTCCATGGTGGAGACACAG                         GACTCTTCAGTAATTGCTCAATTAGGCTGGCCAGACATGCGGCTTCCCATC
genomic: TGTTGTCCATCCCCAAT-CAATCATTCATTCCATGGTGGAGACACAGgtaactctca ... tgttttatagGACTCTTCAGTAATTGCTCAATTAGGCTGGCCAGACATGCGGCTTCCCATC
EST: gi|162185513|gb|FC361237.1|FC361237
EST:     ATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAG                         GACTCTTCAGTAATTGCTCAATTAGGCTGGCCAGACATGCGGCTTCCCATC
genomic: ATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctca ... tgttttatagGACTCTTCAGTAATTGCTCAATTAGGCTGGCCAGACATGCGGCTTCCCATC
EST: gi|162163958|gb|FC339868.1|FC339868
EST:     ATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAG                         GACTCTTCAGTAATTGCTCAA
genomic: ATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctca ... tgttttatagGACTCTTCAGTAATTGCTCAA
EST: gi|162179791|gb|FC356382.1|FC356382
EST:     CCATCCCCAATC-ATCATTTCATTCCATGGTGGAGACACAG                         GACTCTTCAGTAATTGCTCAATTAGGCTGGCCAGACATGCGGCTTCCCATC
genomic: CCATCCCCAATCAATCA-TTCATTCCATGGTGGAGACACAGgtaactctca ... tgttttatagGACTCTTCAGTAATTGCTCAATTAGGCTGGCCAGACATGCGGCTTCCCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctcatgtttgacatgtagattttttttccaaaccatttgtgaataggtcatagttcaccaagagctcagaatgtagacttttgcttttgtcacattggttatacaattgctgacttctgggatgatgtctgtatcctctgttttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA