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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattttatcttgtgtggacacgagaattgttgcttgctgagaagttgcgatccccctcgaagttttaagatctttctccttttttatagttttgcatcgtcccgcctaagtcccgacgtgaataacctgtgaaccgcctttataatgcagGTAGCTATTGTTGTAGGAGGTGGTAATTTCTTCCGAGGAGCAAGCTGGGTTGGTGCCAGTGGACTTGATCGTGCATCAGCCGACCAGATAGG

Basic information

species Physcomitrella patens
transcript PP1S241_40V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S241_40V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ09173 (Selaginella moellendorffii), 3'ss of exon 2
gtgattttatcttgtgtggacacgagaattgttgcttgctgagaagttgcgatccccctcgaagttttaagatctttctccttttttatagttttgcatcgtcccgcctaagtcccgacgtgaataacctgtgaaccgcctttata---atgcagGTAGCTATTGTTGTAGGAGGTGGTAATTTCTTCCGAGGAGCAAGCTGGGTTGGTGCCAGTGGACTTGATCGTGCATCAGCCGACCAGATAGG
                                                                                   |    |   || |  |  ||    | |  |||| | |     ||    | || |  |||| |    || ||| | || || |||||||| ||||| ||||| ||||| ||||||| |||||  |||||||||||||| |||||||| || || || || || ||
------------------------------------------------------------------------------gtaactgccgttacttggttttctcgattccagttcccaagg-----aattctttaatcctctttgtttgcatccagATTGCCATGGTTGTAGGCGGTGGGAATTTTTTCCGGGGAGCAAACTGGGCCGGTGCCAGTGGACTCGATCGTGCCTCGGCAGATCATATCGG

upper sequence: PP1S241_40V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ07189 (Selaginella moellendorffii), 3'ss of exon 2
gtgattttatcttgtgtggacacgagaattgttgcttgctgagaagttgcgatccccctcgaagttttaagatctttctccttttttatagttttgcatcgtcccgcctaagtcccga-cgtgaataacctgtgaaccgcctttata---atgcagGTAGCTATTGTTGTAGGAGGTGGTAATTTCTTCCGAGGAGCAAGCTGGGTTGGTGCCAGTGGACTTGATCGTGCATCAGCCGACCAGATAGG
                                                                                     | |  |   |  || |     |   | ||| |  |   |  ||    | || |  |||| |    || ||| | || || |||||||| ||||| ||||| ||||| ||||||| |||||  |||||||||||||| |||||||| || || || || || ||
------------------------------------------------------------------------------------gtaactgccgttaattggttttctcgattccagttcccaaggaattctttaatcctctttgtttgcatccagATTGCCATGGTTGTAGGCGGTGGGAATTTTTTCCGGGGAGCAAACTGGGCCGGTGCCAGTGGACTCGATCGTGCCTCGGCAGATCATATCGG
















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|100403657|gb|BY955036.1|BY955036
EST:     CAATGGCAATTGCTCGAGAAGTAGCAGCCATAACACGATTGGGTGTGGAG                         GTAGCTATTGTTGTAGGAGGTGGTAATTTCTTCCGAGGAGCAAGCTGGGTT
genomic: CAATGGCAATTGCTCGAGAAGTAGCAGCCATAACACGATTGGGTGTGGAGgtgattttat ... tataatgcagGTAGCTATTGTTGTAGGAGGTGGTAATTTCTTCCGAGGAGCAAGCTGGGTT
EST: gi|162189095|gb|FC365213.1|FC365213
EST:     CAATGGCAATTGCTCGAGAAGTAGCAGCCATAACACGATTGGGTGTGGAG                         GTAGCTATTGTTGTA
genomic: CAATGGCAATTGCTCGAGAAGTAGCAGCCATAACACGATTGGGTGTGGAGgtgattttat ... tataatgcagGTAGCTATTGTTGTA
EST: gi|208365430|gb|DC950897.1|DC950897
EST:     CAATGGCAATTGCTCGAGAAGTAGCAGCCATAACACGATTGGGTGTGGAG                         GTAGCTATTGTTGTAGGAGGTGGTAATTTCTTCCGAGGAGCAAGCTGGGTT
genomic: CAATGGCAATTGCTCGAGAAGTAGCAGCCATAACACGATTGGGTGTGGAGgtgattttat ... tataatgcagGTAGCTATTGTTGTAGGAGGTGGTAATTTCTTCCGAGGAGCAAGCTGGGTT
EST: gi|100373420|gb|BY949317.1|BY949317
EST:     CAATGGCAATTGCTCGAGAAGTAGCAGCCATAACACGATTGGGTGTGGAG                         GTAGCTATTGTTGTAGGNAG-TGGTAATTTCTTCCCGAGNAGCA-GCTGGG
genomic: CAATGGCAATTGCTCGAGAAGTAGCAGCCATAACACGATTGGGTGTGGAGgtgattttat ... tataatgcagGTAGCTATTGTTGTAGG-AGGTGGTAATTTCTTCC-GAGGAGCAAGCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgtcccgcctaagtcccgacgtgaataacctgtgaaccgcctttataatgcagGTAGCTATTGTTGTAGGAGGTGGTAATTTCTTCCGAGGAGCAAGCTGGGTTGGTGCCAGTGGACTTGATCGTGCATCAGCCGACCAGATAGG
                        gaataac  putative branch site (score: 2)
                                      ccgccttt  putative PPT
                                           tttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattttatcttgtgtggacacgagaattgttgcttgctgagaagttgcgatccccctcgaagttttaagatctttctccttttttatagttttgcatcgtcccgcctaagtcccgacgtgaataacctgtgaaccgcctttataatgcagGTAGCTATTGTTGTAGGAGGTGGTAATTTCTTCCGAGGAGCAAGCTGGGTTGGTGCCAGTGGACTTGATCGTGCATCAGCCGACCAGATAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA