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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccacgggctgctgcgtaaagactgtatcctttgtccgtggccgaaaggtgctgtaccctgctgacgcatttgctcgccgctgctcccacatgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGACCCCGACACCTTCGCTGAGCTGAAGGTGAAGGAGATCAAGAACGGCCGCC

Basic information

species Chlamydomonas reinhardtii
transcript EDP01724
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP01724 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GLYMA16G27990.1 (Glycine max), 3'ss of exon 1
gccacgggctgctgcgtaaag--actgtatcc--tttgtcc-----gtggccgaaaggtgctgtaccctgctgacgcatttgctcgccgctgctcccacatgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCG-ACCCCCTGGGCCTGG-CTGACGACCCCGACACCTTCGCTGAGCTGAAGGTGAAGGAGATCAAGAACGGCCGCC
     ||||  ||  || | |  |||| ||||  | | |||     |  ||    |     ||   | |||||| | |       ||   ||||           | |||| | |  | |    ||   || |  |     | |   |  |||  |       | | ||  |  |         |||  | |||     ||||   |    
---gtgggcctcttggtgaggtgactg-atccaatctatccaggtggcagctttgacccattgggtcttgctgatg-acccagaggcttttgctgagCTGAAGGTGAAGGAGCTCAAGAAT---GGTAGGTTGGCCATGTTCTCCATGTTTGGATTCTTTGTTCAGGCAATTGTGAC-------AGGAAAGGGACCCTTAGAAAACC----

upper sequence: EDP01724 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: PP1S169_127V6.1 (Physcomitrella patens), 3'ss of exon 1
gccacgggctgctgcgtaaagactgtatcctttgtccgtggccgaaaggtgctgtaccctgctgacgcatttgctcgccgctgctcccacatgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGC--CTGGCTGAC-GACCCCGACACCTTCGCTGAGCTGAAGGTGAAGGAGATCAAGAACGGCCGCC
||||  |    |  | |   | |||  |     ||    ||     | |  | ||    ||   | | |||  | ||   | | | |    | || ||      | ||| |           | || ||   |||| ||  ||  ||  | || ||||  |||  |   |  |||  ||   |    | |||   |  || | 
gccaatgatctcgacatctcg-ctgagttgaaggtg-aaggagatcaagaacggttgtttgacaatgtattc-cacgtt-cggattctttgttcagGCTATCGTCACTGGA----AAGAGACCCTTGGAGAACCTGAGCGACTATCTTGCAGATCCCGGTACCAACAACGC-CTG--GGCATACACCACCAACTTCACCCCCG
















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|7616109|gb|AW721549.1|AW721549
EST:     GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTG                         GACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGAC
genomic: GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTGgtgagctggg ... atgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGAC
EST: gi|7616319|gb|AW721759.1|AW721759
EST:     GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTG                         GACCCCCTGTACCCCGGCGAG
genomic: GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTGgtgagctggg ... atgcacgcagGACCCCCTGTACCCCGGCGAG
EST: gi|7426880|gb|AW661053.1|AW661053
EST:     GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCACGCTGGCGAGGGCCTG                         GACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGAC
genomic: GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTGgtgagctggg ... atgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGAC
EST: gi|7427096|gb|AW661269.1|AW661269
EST:     GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTG                         GACCCCCTGTACCCCGGCGA
genomic: GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTGgtgagctggg ... atgcacgcagGACCCCCTGTACCCCGGCGA
EST: gi|7615707|gb|AW721147.1|AW721147
EST:     GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTG                         GACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGA
genomic: GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTGgtgagctggg ... atgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGA
EST: gi|7426881|gb|AW661054.1|AW661054
EST:     GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTG                         GACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGAGCCTGGCTGACGAC
genomic: GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTGgtgagctggg ... atgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGAC
EST: gi|7616235|gb|AW721675.1|AW721675
EST:     GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTG                         GACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGAC
genomic: GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTGgtgagctggg ... atgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGAC
EST: gi|7427390|gb|AW661556.1|AW661556
EST:     GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTG                         TACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGA
genomic: GCCTGGTCGAGGGCTACCGCGTTAACGGCGGCCCCGCTGGCGAGGGCCTGgtgagctggg ... atgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtgctgtaccctgctgacgcatttgctcgccgctgctcccacatgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGACCCCGACACCTTCGCTGAGCTGAAGGTGAAGGAGATCAAGAACGGCCGCC
              tgctgac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccacgggctgctgcgtaaagactgtatcctttgtccgtggccgaaaggtgctgtaccctgctgacgcatttgctcgccgctgctcccacatgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGCCTGGCTGACGACCCCGACACCTTCGCTGAGCTGAAGGTGAAGGAGATCAAGAACGGCCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - -aaagact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acgcatt