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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgctctcatccttacttcgtaaatctttaccagttgataatgatttatggcttttactaccacacacaagcgcacatgtcaatgcttcctcccatgaaactacataactcagcctgaataactcttgtagttgtgcatttgagtttgaataactcgaatcgcttttgagtgcagATTGTTAACAGGGTCTATCCTGGCTCACGAACTGATGCACGCATGGATTCGTCTCGACG

Basic information

species Physcomitrella patens
transcript PP1S231_3V6.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S231_3V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA02G06720.1 (Glycine max), 3'ss of exon 9
gtgtgctctcatccttacttcgtaaatctttaccagttgataatgatttatggcttttactaccacacacaagcgcacatgtcaatgcttcctcccatgaaactacataact-cagcctgaataactcttgtagttgtgcatttgagtttga-ataactcgaatcgcttttgagtgcagATTGTTAACAGGGTCTATCCTGGCTCACGAACTGATGCACGCATGGATTCGTCTCGACG
                                                                                      |  |||| |  ||| |     ||  | ||   |  |||  | ||| |  | || | || | | | | |||| || |     || |      || || || || || || ||||||||||||||| |||||||||||||| || | ||  | |
--------------------------------------------------------------------------------------gtatccttc--tgatatcgtctattttcaaaatctatagtttttgca--tatggaattcactctaatataattcaaggattttatattgatagGTTATTGACTGGATCAATCCTGGCTCACGAAATGATGCACGCATGGCTTAGACTTAAAG
















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|208394621|gb|DC928781.1|DC928781
EST:     ACACGGCATTGCGAGGTCACAGCCATTCTTGTTCTATATGGTTTACCTAG                         ATTGTTAACAGGGTCTATCCTGGCTCACGAACTGATGCACGCATGGATTCG
genomic: ACACGGCATTGCGAGGTCACAGCCATTCTTGTTCTATATGGTTTACCTAGgtgtgctctc ... ttgagtgcagATTGTTAACAGGGTCTATCCTGGCTCACGAACTGATGCACGCATGGATTCG
EST: gi|208391911|gb|DC949374.1|DC949374
EST:     ACACGGCATTGCGAGGTCACAGCCATTCTTGTTCTATATGGTTTACCTAG                         ATTGTTAACAGGGTCTATCCTGGCTCACGAACTGATGCACGCATGGATTCG
genomic: ACACGGCATTGCGAGGTCACAGCCATTCTTGTTCTATATGGTTTACCTAGgtgtgctctc ... ttgagtgcagATTGTTAACAGGGTCTATCCTGGCTCACGAACTGATGCACGCATGGATTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcttgtagttgtgcatttgagtttgaataactcgaatcgcttttgagtgcagATTGTTAACAGGGTCTATCCTGGCTCACGAACTGATGCACGCATGGATTCGTCTCGACG
                           gaataac  putative branch site (score: 2)
                                       tcgctttt  putative PPT
                        tttgaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgctctcatccttacttcgtaaatctttaccagttgataatgatttatggcttttactaccacacacaagcgcacatgtcaatgcttcctcccatgaaactacataactcagcctgaataactcttgtagttgtgcatttgagtttgaataactcgaatcgcttttgagtgcagATTGTTAACAGGGTCTATCCTGGCTCACGAACTGATGCACGCATGGATTCGTCTCGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA