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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgagctattctattatttaggatctgcttagcacaagcacgatgtttatcgctcttactctctgatgaatctctttacacacctatttggtagtattctctgacactttgtgttgatgccattactttgcttctacctgctgtgtgcattgattggattttgattgaatgtatgcatagGGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTGGATCCTGATG

Basic information

species Physcomitrella patens
transcript PP1S152_87V6.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S152_87V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 8
gtaagcgagctattctattatttaggatctgcttagcacaagcacgatgtttatcgctcttactctctgatgaatctctttacacacctatttggtagtattctctgacactttgtgttgatgccattactttgcttctacctgctgtgtgcattgattggattttgattgaatgtatgcatagGGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTGGATCCTGATG
                                                           |||   ||  |     |   |   | | | |     | ||     ||  ||    |  |  ||   |  |   || || ||     ||| ||  |   ||   ||||| || |   || |           || ||  | || || || || ||||||||||||||||||||||| || |||||||
-----------------------------------------------------------ttaaggtccaagaggaccagtacaaaaaccaccctatggtgg---ctagcaacaagcataaataaaagaa---tggtttta-----tgtttgtttctgtt---ttttgtttcagGATAAG-----------GTACTCAAACCATTAGGAGCTGTTACCACTGGAAGTCAATTCCTTGAGCCTGATG
















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|162196622|gb|FC374912.1|FC374912
EST:     GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCA                         GGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTG
genomic: GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCAgtaagcgagc ... gtatgcatagGGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTG
EST: gi|100352594|gb|BY945350.1|BY945350
EST:     GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCA                         GGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTG
genomic: GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCAgtaagcgagc ... gtatgcatagGGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTG
EST: gi|162196876|gb|FC375153.1|FC375153
EST:     GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCA                         GGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTG
genomic: GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCAgtaagcgagc ... gtatgcatagGGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTG
EST: gi|162215700|gb|FC391415.1|FC391415
EST:     GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCA                         GGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTG
genomic: GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCAgtaagcgagc ... gtatgcatagGGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTG
EST: gi|162159476|gb|FC336265.1|FC336265
EST:     GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCA                         GGGCGTGTCCTGGAGCCTTTGGNGGCAGTTACCACTGGAAGTCA-TTCCCT
genomic: GATTTCACATAGTTGTGGACGCAGGGAATGGGGCAGGCGGCTTCTTCGCAgtaagcgagc ... gtatgcatagGGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCC-T


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgcttctacctgctgtgtgcattgattggattttgattgaatgtatgcatagGGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTGGATCCTGATG
                                 ttttgat  putative branch site (score: 4)
                                attttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgagctattctattatttaggatctgcttagcacaagcacgatgtttatcgctcttactctctgatgaatctctttacacacctatttggtagtattctctgacactttgtgttgatgccattactttgcttctacctgctgtgtgcattgattggattttgattgaatgtatgcatagGGGCGTGTCCTGGAGCCTTTGGGGGCAGTTACCACTGGAAGTCAATTCCTGGATCCTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG