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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttcctttccatttgtgtgttttgatcttgtaattctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTG

Basic information

species Selaginella moellendorffii
transcript EFJ31523
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31523 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: LOC_Os10g27220.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------gtaagtgtttcctttccatttgtgtgttttgatcttgtaattctattg-gcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTG
                                                 || |||       |    | |       |    ||||   |  | ||| | ||||  | |   |||| ||  | || ||| | || |||||| | || ||||||||||||||||| || ||||| |||||||||||||||||| | ||| |||
cagcagtcttatctggtttgttatatttatttcttgcataacttatttggttagtacaatgctgaactgtaaacagctgacacttgc--tcatgttgtgtagGTTGCTAGCTTAGTTAAGAAAGGTGCCCATAAGATAACTCTCAGTATTGGTGATGGTGCTAATGATGTGAGTATGATTCAAGCTGCTCATGTGGGGATTG

upper sequence: EFJ31523 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GRMZM2G020553_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------gta-agtgtttcctttccatttgtgtgttttgatcttgt-aat-tctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTG
                                             | | ||| ||   |         | |    || |    | ||| | |||  | |||| || |   |||| |   | || ||  ||||||||||| | ||||||||||| |||||||| || ||||| |||||||||||||||||| | ||| |||
aagcaaatgggggcaatagtctctgattgattgcatggtttcattgcacagtcttgtatacgtgaaaatataaaatgctgacattaatgtgtatatgtagGTTACAAGCTTAGTTAGGAAGGGTGCTGAGAAAATAACTCTCAGCATTGGTGACGGTGCTAATGATGTGAGTATGATTCAAGCTGCTCATGTTGGGATTG

upper sequence: EFJ31523 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA08G40530.1 (Glycine max), 3'ss of exon 22
-----------------------------------------------gtaagtgtttcctttccatttgtgtgtt-ttgatcttgtaattctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTG
                                               ||  ||       |   | || |   || ||  |    ||  ||| ||  ||||| ||||   | || ||  | || ||  | ||||||||  | || ||||||||||| || || || || ||||||||||||||||||||| | |||||||
gcttagtgagtaggagtgcttaaagtaattgcctagtagaatttggcgttggttagcttatgaaaattttccattatttgttcactatatctgtttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGGGTTG

upper sequence: EFJ31523 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA18G16990.1 (Glycine max), 3'ss of exon 14
--------------------------------------------gtaagtgtttcctttcc----atttgtgtgttttgatcttgtaattctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTG
                                            |    |||||   ||      ||||     | ||  |    ||  |||  |  ||||| ||||   | || ||  | || ||  | ||||| ||  | || ||||||||||| || || || || ||||||||||||||||||||| | || ||||
cttagtgagtaggagttgcttaaagtaactgcctagtagaatttggcgttgtttagcttatgaaaattttccattatttgttcactatatctgcttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATTACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGCGTTG

upper sequence: EFJ31523 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: Vv00s0189g00030.t01 (Vitis vinifera), 3'ss of exon 21
------------------------------------gtaagtgtttcctttccatttgtgtgttttgatcttgtaatt-ctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTG
                                    |     || || | || |  ||  | ||  ||  |    |||  | || | |||| || |  || || ||  | || ||   |||||||||  | || |||||||||||||| || ||||| |||||||||||||| |||||| | || ||||
gtaagatgttttattttgttgttttgaagcaacttggctgaagtatcatgtc-agctgaatattgagaaatcactattgttgtttgtagGTGACAAGCCTGGTCAAGAAAGGTGCACGGAAAATAACACTTAGTATTGGTGATGGTGCCAATGACGTCAGCATGATTCAAGCGGCTCATGTTGGCGTTG

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|169038590|gb|FE447422.1|FE447422
EST:     AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAA                         GTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT
genomic: AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAAgtaagtgttt ... ctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT
EST: gi|169108451|gb|FE510445.1|FE510445
EST:     AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAA                         GTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT
genomic: AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAAgtaagtgttt ... ctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT
EST: gi|169055982|gb|FE466171.1|FE466171
EST:     AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAA                         GTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT
genomic: AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAAgtaagtgttt ... ctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT
EST: gi|169088452|gb|FE495498.1|FE495498
EST:     AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAA                         GTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT
genomic: AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAAgtaagtgttt ... ctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT
EST: gi|169106117|gb|FE507935.1|FE507935
EST:     AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAA                         GTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT
genomic: AGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAAgtaagtgttt ... ctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGT

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: 30 (upstream exon), 34 (downstream exon)
Score: 16

GTTTGCGCTGGATTCTCCGTTACGCGCCACTCTCTTGAAACTGGGAATTAAGTGCAAGGCTGTTGTGTGCTGTCGAGTTTCTCCATTGCAGAAAGCTCAAgtaagtgttt ... ctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtgtttcctttccatttgtgtgttttgatcttgtaattctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTG
                             ttttgat  putative branch site (score: 16)
                                           ttctatt  putative PPT
                                        taattctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttcctttccatttgtgtgttttgatcttgtaattctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT