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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatataccggtcttgtcacccgttttttctgcaattcctcgcttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGGCTGTCGAAGAAAGTGGATGCCATCAAGGAAACGCTTGAAAACCAGGAGC

Basic information

species Selaginella moellendorffii
transcript EFJ16507
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 10
--------------------------------------------------------------------------------------------gtaatat-accggtcttgtcacccgttttttctgcaattcctcgcttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGGCTGTCGAAGAAAGTGGATGCCATCAAGGAAACGCTTGAAAACCAGGAGC
                                                                                             | |||| | || |||| |  |      | | |  |   | ||   |||  |||||||||||||||||||| || ||||||||||||||     ||||| |||| ||| |    | ||| || ||||||||||| |  || || ||  | ||||
gttagtctgttgttataactgctttgagatagaaatagattaatgtttgcttcttaaggaagaaaaattaaggtagtttgttgctcactgagttgatatcaacgttcttctggctttggatctttaaaccgcttcctctttgtcagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGC

upper sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------------------------------gtaatataccggtcttgtcacccgttttttctgcaattcctcgcttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGGCTGTCGAAGAAAGTGGATGCCATCAAGGAAACGCTTGAAAACCAGGAGC
                                                                                                ||   |      | | || |    |   |        ||||   | ||   ||||||||||||||||||| || ||||||||||||||     | |||||| ||||  |    ||||| |||||||||||||| || || || ||| | ||||
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC

upper sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 9
-------------------------------------------gtaatataccggtcttgtcacccgttttttct----gcaattcctcgcttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGGCTGTCGAAGAAAGTGGATGCCATCAAGGAAACGCTTGAAAACCAGGAGC
                                           |    || |   ||| || ||   | | |       |   || ||  || ||| |||||||| ||||||||||| || ||||||||||||||     |||||||| ||||  |    ||||| || ||||||||||| || || || ||| | ||||
atcactccatactccttgcttcttgaaacattctgtattttctgctgaattctcttctggttacatatgtatcactaaagttgtttctttctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGC

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|169030583|gb|FE439541.1|FE439541
EST:     AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAG                         GCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG
genomic: AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAGgtaatatacc ... cttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG
EST: gi|169072619|gb|FE481584.1|FE481584
EST:     AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAG                         GCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG
genomic: AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAGgtaatatacc ... cttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG
EST: gi|169072620|gb|FE481585.1|FE481585
EST:     GCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCNTAA-TGCAACANAG                         GCTGCTGTTTGAG-AAGGCATCGTTGTTGGT
genomic: GCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTC-TAAATGCAACAAAGgtaatatacc ... cttttcgcagGCTGCTGTT-GAGGAAGGCATCGTTGTTGGT
EST: gi|169088884|gb|FE494422.1|FE494422
EST:     AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAG                         GCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG
genomic: AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAGgtaatatacc ... cttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG
EST: gi|169082801|gb|FE486256.1|FE486256
EST:     AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAG                         GCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG
genomic: AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAGgtaatatacc ... cttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG
EST: gi|169076090|gb|FE484392.1|FE484392
EST:     AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAG                         GCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG
genomic: AGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAGgtaatatacc ... cttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGG

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: 35 (upstream exon), 35 (downstream exon)
Score: 95

GTGGGAGCTCAAACGGAAACCGAGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAGgtaatatacc ... cttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGGCTGTCGAAGAAAGTGGATGCCATCAAGGAAACGCTTGAAAACCAGGAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatataccggtcttgtcacccgttttttctgcaattcctcgcttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGGCTGTCGAAGAAAGTGGATGCCATCAAGGAAACGCTTGAAAACCAGGAGC
                                       ttcctcgcttttcgc  CT-rich tract
                          ttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatataccggtcttgtcacccgttttttctgcaattcctcgcttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGGCTGTCGAAGAAAGTGGATGCCATCAAGGAAACGCTTGAAAACCAGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA