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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGAACCAACCGCGGCATCTCTTGCTTACGGGTTTGAGAGGAAGAGTAATGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtctattactgatcaagtgttggttcttaactctggaatcttttctcttcag

Basic information

species Selaginella moellendorffii
transcript EFJ23703
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23703 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv18s0041g01230.t01 (Vitis vinifera), 5'ss of exon 2
AACGAACCAACCGCGGCATCTCTTGCTTACGGGTTTGAGAGGAAGAGTAATGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtctattactgatcaagtgttggttcttaactc-tggaatcttttct------cttcag-----------------------------------
|| ||||| || || || || || || || || ||||| | ||||| |||||| |||||||| || |||||| | || ||||| ||||| ||||||||||||  |||    |||  | | |   | ||  | |  | |   |||||||  ||||       || |                                    
AATGAACCTACTGCAGCTTCACTGGCATATGGTTTTGAAAAGAAGAATAATGAAACAATTCTTGTATTTGATCTTGGAGGTGGTACATTTGATGTTTCAGgtatgagaatcatt-ttaagctcattttcatccaaatcaggtggaatcgattctgagaccttttaaggaaataagtttgttaatttttatgccatctcatc
















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|169104027|gb|FE505040.1|FE505040
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169029193|gb|FE439399.1|FE439399
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169047500|gb|FE455695.1|FE455695
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169081877|gb|FE486424.1|FE486424
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169079168|gb|FE488653.1|FE488653
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169082126|gb|FE490586.1|FE490586
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169041609|gb|FE448218.1|FE448218
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCTAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169022591|gb|FE429670.1|FE429670
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169051045|gb|FE458215.1|FE458215
EST:     GCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: GCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169021803|gb|FE429917.1|FE429917
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
EST: gi|169082946|gb|FE491146.1|FE491146
EST:     TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAG                         TTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA
genomic: TGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATA

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), 34 (downstream exon)
Score: 45

AACGAACCAACCGCGGCATCTCTTGCTTACGGGTTTGAGAGGAAGAGTAATGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtc ... ttctcttcagTTTTGGAAGTCGGCGATGGTGTGTTCGAAGTGTTATCAACATCTGGTGATACACACTTGGGTGGAGACGATTTTGACAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGAACCAACCGCGGCATCTCTTGCTTACGGGTTTGAGAGGAAGAGTAATGAGACAATTCTCGTCTTTGATTTGGGCGGTGGAACATTCGATGTTTCAGgtgagaggtctattactgatcaagtgttggttcttaactctggaatcttttctcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA