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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatggacatgggcttgtgtcatggtggtttcttcagacgctagaatcacttgggtatgtatgtatggcctatgtggatattgatgggaatttctttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAGTGTTGCAATTGAAACGAAG

Basic information

species Physcomitrella patens
transcript PP1S90_220V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S90_220V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 8
gatggacatgggcttgtg-tcatggtggtttcttcagacgctagaatcacttgg-gtatgtatgtatggcctatgtggatattga----tgggaatttctttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAGTGTTGCAATTGAAACGAAG
        |||  |  |  || | |     | |  ||     |  | ||||||  || | ||  | |      | |    ||  |    |   |  ||   | |||||| ||| | ||||| || || ||||| ||||| |||||||| ||||||||||| ||||||||  |   |
------tttggtttcttaatctttgaaaagtatatagctctgaacaacacttgctgtgtctacttttcattccttttttcatcaaatcttattagcttgcattcagGGCAGATTCTGCAGCTGTGGCAATCACCACTACAGATCTTGTTAGCAAGAGTGTGGCAATTGAGTCTCTG

upper sequence: PP1S90_220V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT2G37500.1 (Arabidopsis thaliana), 3'ss of exon 8
gatggacatgggcttgtgt-catggtggtttcttcagacgctagaatcac----ttgggtatgtatgtatggcctatgtggatattgatgggaatttct--ttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAGTGTTGCAATTGAAACGAAG
       ||   ||| | | |    |   |  || |    |     ||||    ||   | | | ||  | |||  || | |||   ||  |||| |     |||||||| ||| | || || ||||| |||||||| || |||||||| ||||||||||||||| ||||| |  ||
-----gtataatcttcttttctcaatctctcttttaagttcgtaggtcacagtcttcactttctttg-gtagccattgggcataaccatatgaatgttgaaatgcagGGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAAGCAAGAGTGTTGCAGTTGAATCACAG
















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|162173818|gb|FC349410.1|FC349410
EST:     ATTGAAGCCGTGCCGAAGTTGGTGGGGTCTTTATCTGCAAGTGTTGCATC                         GGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAG
genomic: ATTGAAGCCGTGCCGAAGTTGGTGGGGTCTTTATCTGCAAGTGTTGCATCgtgagttcag ... ttctttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAG
EST: gi|162169383|gb|FC345739.1|FC345739
EST:     ATTGAAGCCGTGCCGAAGTTGGTGGGGTCTTTATCTGCAAGTGTTGCATC                         GGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAG
genomic: ATTGAAGCCGTGCCGAAGTTGGTGGGGTCTTTATCTGCAAGTGTTGCATCgtgagttcag ... ttctttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAG
EST: gi|162152901|gb|FC329203.1|FC329203
EST:     ATTGAAGCCGTGCCGAAGTTGGTGGGGTCTTTATCTGCAAGTGTTGCATC                         GGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAG
genomic: ATTGAAGCCGTGCCGAAGTTGGTGGGGTCTTTATCTGCAAGTGTTGCATCgtgagttcag ... ttctttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAG
EST: gi|162186918|gb|FC362596.1|FC362596
EST:     ATTGAAGCCGTGCCGAAGTTGGTGGGGTCTTTATCTGCAAGTGTTGCATC                         GGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAG
genomic: ATTGAAGCCGTGCCGAAGTTGGTGGGGTCTTTATCTGCAAGTGTTGCATCgtgagttcag ... ttctttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttgggtatgtatgtatggcctatgtggatattgatgggaatttctttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAGTGTTGCAATTGAAACGAAG
                                tattgat  putative branch site (score: 3)
                                            tttctttgc  putative PPT
                                          aatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatggacatgggcttgtgtcatggtggtttcttcagacgctagaatcacttgggtatgtatgtatggcctatgtggatattgatgggaatttctttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAGTGTTGCAATTGAAACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA