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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgacttttcttctagcctactcgtgtcttctcttctgcaatagtgttcttggtcgtaaaagtttcgtgatcattctaaatgcctactactcacactggcattgtgtatgaacagCGAGGGAAGGCTGGTGCATATCGATTTTGGCTTCATACTTGAAACTTCCCCTGGAGGCAACATGCGATTTGAGAGTGCAGACTTCAAATTGAGTCATGAG

Basic information

species Physcomitrella patens
transcript PP1S93_76V6.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S93_76V6.1 (Physcomitrella patens), 3'ss of exon 24
lower sequence: AT1G49340.2 (Arabidopsis thaliana), 3'ss of exon 24
----------------------gtacgacttttcttctagcctactcgtgtcttctcttctgcaatagtgt---------tcttggtcgtaaaa----gtttcgtgatcattctaaatgcc-tactactc--acactg-gcattgtgtatgaacagCGAGGGAAGGCTGGTGCATATCGATTTTGGCTTCATACTTGAAACTTCCCCTGGAGGCAACATGCGATTTGAGAGTGCAGACTTCAAATTGAGTCATGAG
                       | |   | |||||  |  ||   |   |  |   ||    || ||| |         ||| | | | ||||    || | |  |   |  |  | |    || |||     ||   |  || ||      ||||| |||||| || || || ||||| ||||| |||||  | |||||||| ||||| || ||||||||||| ||||||||  | |||||| |||| || || 
gtatgtttcctatttttgcacattccctttgttctttgattctttccacttggtgcattggaaaaaagtttatcaaaacctctcgatggaaaaatatagtgttggaaatttcatggaagtaacacaactttattaccatgtgttatgctaatgcagCGTGGGAAGACTTGTCCACATCGACTTTGGTTTCATTTTGGAAACTTCGCCTGGTGGGAACATGCGATTCGAGAGTGCTCATTTCAAACTGAGCCACGAA

upper sequence: PP1S93_76V6.1 (Physcomitrella patens), 3'ss of exon 24
lower sequence: Vv03s0063g02260.t01 (Vitis vinifera), 3'ss of exon 24
gtacgacttttcttctagcctactcgtgtcttctcttctgcaatagtgttcttggtcgtaaaagtttcgtgatcattctaaatgcctactactcacactggcattgtgtatgaacagCGAGGGAAGGCTGGTGCATATCGATTTTGGCTTCATACTTGAAACTTCCCCTGGAGGCAACATGCGATTTGAGAGTGCAGACTTCAAATTGAGTCATGAG
     |||| | |  |||    | | | |  |  | | || | ||    | |||   ||| ||||   |     | |  || | || | || | |        |  |||     ||| ||||||||||| || |||||||||||||| || ||||| |||||||| ||||| || || ||||||||||| |||||  |||||||  |||| ||||||
----tacttatataatagatggcccatataatggcatttg-acta----tattgcctgtataagtactgcagaaaatgcaagtcccaattaataa--------tcatgttcatgcagGGAGGGAAGGCTTGTTCATATCGATTTTGGTTTTATACTGGAAACTTCACCTGGTGGAAATATGCGATTTGAAAGTGCCCACTTCAAGCTGAGCCATGAG
















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|67698973|gb|BJ959206.1|BJ959206
EST:     CTTCTGCTCCAACCAAAGGACCGACACAATGGAAATCTTTTATTTGACAA                         CGAGGGAAGGCTGGTGCATATCGATTTTGGCTTCATACTTGAAACTTCCCC
genomic: CTTCTGCTCCAACCAAAGGACCGACACAATGGAAATCTTTTATTTGACAAgtacgacttt ... gtatgaacagCGAGGGAAGGCTGGTGCATATCGATTTTGGCTTCATACTTGAAACTTCCCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttcgtgatcattctaaatgcctactactcacactggcattgtgtatgaacagCGAGGGAAGGCTGGTGCATATCGATTTTGGCTTCATACTTGAAACTTCCCCTGGAGGCAACATGCGATTTGAGAGTGCAGACTTCAAATTGAGTCATGAG
                           tactcac  putative branch site (score: 1)
            attctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgacttttcttctagcctactcgtgtcttctcttctgcaatagtgttcttggtcgtaaaagtttcgtgatcattctaaatgcctactactcacactggcattgtgtatgaacagCGAGGGAAGGCTGGTGCATATCGATTTTGGCTTCATACTTGAAACTTCCCCTGGAGGCAACATGCGATTTGAGAGTGCAGACTTCAAATTGAGTCATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG