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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttctacaccctcagattatacacgagcgggagtttcctgtcaaaactcaagctgtgaagagtgatgtatgaagtcgttaatgtacttgagtgatacagATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGGCTGTTTCTTTTGTGTGAAG

Basic information

species Physcomitrella patens
transcript PP1S95_68V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S95_68V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv07s0031g03150.t01 (Vitis vinifera), 3'ss of exon 2
--ggttctacaccctcagattatacacgagcgggagtttcctgtcaaaactcaagctgtgaagagtgatgtatgaagtcgttaat-gtacttgagtgatacagATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGGCTGTTTCTTTTGTGTGAAG
    || |||    |   ||| |  | |    |||     ||   ||| |  |||     || |  |||| |||   |    | |   |  |   || | |||||| ||| | || || || ||||| || || |||||||||||||||||| |||||||||| |||   | |
gtttttttacttttttgaattgt-tatgttatgga----tctaagaaagcaaaagaataaaaaaaagatg-atggcatgaccatttaaaggtttatgtttcagATTTCCTATTGGATCTCGTGTTGTTGGAGCTTTCATCATGCCCTGTGGTAGCTGTTTCTTCTGTAACAGG
















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|162269692|gb|FC444884.1|FC444884
EST:     GGAGAGGTTGTCGAACATGGGAAGCATACCGATTCAGCGACCATCGAGAG                         ATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGG
genomic: GGAGAGGTTGTCGAACATGGGAAGCATACCGATTCAGCGACCATCGAGAGgtatgattca ... agtgatacagATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGG
EST: gi|162188954|gb|FC364344.1|FC364344
EST:     GGAGAGGTTGTCGAACATGGGAAGCATACCGATTCAGCGACCATCGAGAG                         ATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGG
genomic: GGAGAGGTTGTCGAACATGGGAAGCATACCGATTCAGCGACCATCGAGAGgtatgattca ... agtgatacagATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGG
EST: gi|162267940|gb|FC444021.1|FC444021
EST:     GGAGAGGTTGTCGAACATGGGAAGCATACCGATTCAGCGACCATCGAGAG                         ATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGG
genomic: GGAGAGGTTGTCGAACATGGGAAGCATACCGATTCAGCGACCATCGAGAGgtatgattca ... agtgatacagATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGG
EST: gi|67572828|gb|BJ945652.1|BJ945652
EST:     GGAGAGGTTGTCGAACATGGGAAGCATACCGATTCAGCGACCATCGAGAG                         ATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGG
genomic: GGAGAGGTTGTCGAACATGGGAAGCATACCGATTCAGCGACCATCGAGAGgtatgattca ... agtgatacagATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcaagctgtgaagagtgatgtatgaagtcgttaatgtacttgagtgatacagATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGGCTGTTTCTTTTGTGTGAAG
                               cgttaat  putative branch site (score: 4)
                                 ttaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttctacaccctcagattatacacgagcgggagtttcctgtcaaaactcaagctgtgaagagtgatgtatgaagtcgttaatgtacttgagtgatacagATTGCCTGTGGGGTCGCGAGTTGTGGGTGCATTCATCATGCCCTGTGGTGGCTGTTTCTTTTGTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT