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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactacactaccgttgtctttggtttcttctctctttggctcgactgcgcataatgtggtgacatgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACGGGTTCTCGCGTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACA

Basic information

species Selaginella moellendorffii
transcript EFJ10940
intron # 8
splice site 3'
intron type U2

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|169109266|gb|FE514068.1|FE514068
EST:     GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
EST: gi|169029497|gb|FE438897.1|FE438897
EST:     GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
EST: gi|169041054|gb|FE450354.1|FE450354
EST:     GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
EST: gi|169024460|gb|FE434385.1|FE434385
EST:     GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
EST: gi|169106433|gb|FE507445.1|FE507445
EST:     GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
EST: gi|169069401|gb|FE480524.1|FE480524
EST:     ---TCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
EST: gi|169083532|gb|FE495876.1|FE495876
EST:     GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
EST: gi|169069400|gb|FE480523.1|FE480523
EST:     GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
EST: gi|169035072|gb|FE444881.1|FE444881
EST:     GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
EST: gi|169113335|gb|FE515286.1|FE515286
EST:     GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGG                         TTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG
genomic: GGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACG

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: 32 (upstream exon), 33 (downstream exon)
Score: 12

GCGGCTCAGTCATTTCTTTGACGTACATGGCATCTGAAAAAACCATTCCCGGgtaactacac ... catgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACGGGTTCTCGCGTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttggtttcttctctctttggctcgactgcgcataatgtggtgacatgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACGGGTTCTCGCGTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACA
                                 ataatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactacactaccgttgtctttggtttcttctctctttggctcgactgcgcataatgtggtgacatgtaacagTTACGGTGGAGGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACGGGTTCTCGCGTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA