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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacaaagtaataatttttaaagaccggatcgcacaggtcgttcgcattcaatgaattatatgatacgaggccttttctaatagagtggctgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAACTTTGGGTTTTATATCCTCTCCTCTTTATTCTACAG

Basic information

species Physcomitrella patens
transcript PP1S89_217V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S89_217V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G088648_T01 (Zea mays), 3'ss of exon 7
acacaaagtaataatttttaaagaccggatcg-cacaggtcg-ttcgcattcaatgaattatatgatacgaggccttttctaatagagtggctgatgta-------cagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAACTTTGGGTTTTATATCCTCTCCTCTTTATTCTACAG
          |  | ||    ||   |||    |  |  | | || | | ||    | |||    |  | | |  |||| |  ||    |  |  ||         ||||||  ||||||||||||||||||||||||||| || |||||| |||| ||| | | | | || |  |||||||| ||| |  | |||
---------taggacttcaggagttaggacaaacctaaatggatttgtactcgtgtagttactgcagtcaaagtatttttttgtaagtggaattttgcttttcaatcagGCTAAAAGGATGGATGTTGTATGGGGAGAGACTGCTGGTGTTGAAGGTCAATTGTTGCTGTTGTGCCCTCTCCTTTTTCTATTGCAG

upper sequence: PP1S89_217V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G154328_T01 (Zea mays), 3'ss of exon 7
acacaaagtaataatttttaaagaccggatcgcacaggtcgttcgcattcaatgaattatatgatacgaggccttttctaatagagtggctgatgtac----agGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAACTTTGGGTTTTATATCCTCTCCTCTTTATTCTACAG
 ||     ||   |  |    |  |    | |||  |    |   | | |||| || |  |  | | |     |||| |||  |      || | | |    |||||  ||| ||||||||||||||||||||||| || |||||| |||| ||| | | | | || |  |||||||| ||  | || |||
-catggtctaccgacatcactattc---gttgcatggcatttagccgtgcaataaacttaagtaaaagcaatattttgtaactggaattttgctttgccaccagGCTAAAAGAATGGATGTTGTATGGGGAGAGACTGCTGGTGTTGAAGGTCAATTGTTGCTGTTGTGCCCTCTCCTTTTCCTCCTGCAG
















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|208362728|gb|DC947191.1|DC947191
EST:     AGAACCGTTATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAG                         GCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
genomic: AGAACCGTTATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAGgtatgctttt ... tgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
EST: gi|162250599|gb|FC428190.1|FC428190
EST:     ATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAG                         GCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
genomic: ATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAGgtatgctttt ... tgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
EST: gi|162250598|gb|FC428189.1|FC428189
EST:     ACGCCTATATACTCGAATTGCTCTTGGGAAG                         GCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
genomic: ACGCCTATATACTCGAATTGCTCTTGGGAAGgtatgctttt ... tgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
EST: gi|208387444|gb|DC949229.1|DC949229
EST:     GCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAG                         GCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
genomic: GCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAGgtatgctttt ... tgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
EST: gi|208395643|gb|DC924193.1|DC924193
EST:     AGAACCGTTATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAG                         GCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
genomic: AGAACCGTTATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAGgtatgctttt ... tgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
EST: gi|67701379|gb|BJ961612.1|BJ961612
EST:     CTCTTGGGAAGG                         GCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCA
genomic: CTCTTGGGAA-Ggtatgctttt ... tgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCA
EST: gi|208347899|gb|DC917606.1|DC917606
EST:     AGAACCGTTATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAG                         GCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
genomic: AGAACCGTTATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAGgtatgctttt ... tgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
EST: gi|208363415|gb|DC947013.1|DC947013
EST:     AGAACCGTTATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAG                         GCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA
genomic: AGAACCGTTATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAGgtatgctttt ... tgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 35 (downstream exon)
Score: 51

GCGGCTGTTCCTTGGTTGGGCTGTGATGCAAGGTGTGGCTATGCTACTACAGAACCGTTATCAGCGTCGACGCCTATATACTCGAATTGCTCTTGGGAAGgtatgctttt ... tgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAACTTTGGGTTTTATATCCTCTCCTCTTTATTCTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcaatgaattatatgatacgaggccttttctaatagagtggctgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAACTTTGGGTTTTATATCCTCTCCTCTTTATTCTACAG
     aatgaattatatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacaaagtaataatttttaaagaccggatcgcacaggtcgttcgcattcaatgaattatatgatacgaggccttttctaatagagtggctgatgtacagGCTGGAAGGATGGATGTTGTATGGGGAGAGACGGCCGGTGTTAAAGGGCAACTTTGGGTTTTATATCCTCTCCTCTTTATTCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC