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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagcctttcttatcaccttgtttctcatgtgttctttcttacgcgtttgcgtttgtttgtctctagGTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAATCCAAACGTCATGGTCTGTGAGCGCGGCACCATGTTTGGCTACA

Basic information

species Selaginella moellendorffii
transcript EFJ32189
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32189 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os12g10784.3 (Oryza sativa), 3'ss of exon 7
------------gtaagaagcctttcttatcacct-------tgtt--tctcatgtgttctttcttacgcgtttgc--------gtttgtttgtctctagGTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAATCCAAACGTCATGGTCTGTGAGCGCGGCACCATGTTTGGCTACA
              | | |       ||||||| |       ||||  | |   | |   | |||  |  || ||           |||| | | || |||| ||| |||| || || |  || ||||| ||||||||||||| ||| || |||||||||||||| |||||||||||||||||||
ttacctgctttttcaggcaaatccctttatcacatccagttatgttaattttcggaggcatctctagcatgtctgtcataataaacttgtatctttccagGTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACA

upper sequence: EFJ32189 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 7
---------------gtaagaagcctttcttatcaccttgttt-ctcatgtgttctttcttac-gcgtttgcgttt----------gttt--gtctctagGTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAATCCAAACGTCATGGTCTGTGAGCGCGGCACCATGTTTGGCTACA
               |   ||||    |  | | |||   ||| ||  |||    |||||||| || | ||| | |           |||   |||| |||| |||   || ||  | |  ||  | ||||||||||| |||||||| || |||||||||||||| || ||||||||||||||||
atattcctggttaaggcttgaagataattattttaccagatttacttgtgttacttttcttactgcatgtgcttgtcaaagtgaacatttacatctccagGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA
















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|169105840|gb|FE503524.1|FE503524
EST:     AGACCGGCAAAGTGATCAACATNNNNNNNGGCCAGTTTTGCGCTTCCTCT                         GTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAAT
genomic: AGACCGGCAAAGTGATCAACATAAAAAAAGGCCAGTTTTGCGCTTCCTCCgtaagaagcc ... ttgtctctagGTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAAT




















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), 27 (downstream exon)
Score: 6

ACGGATCTTCTTCTCGCAGCTGCTAAGACCGGCAAAGTGATCAACATAAAAAAAGGCCAGTTTTGCGCTTCCTCCgtaagaagcc ... ttgtctctagGTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAATCCAAACGTCATGGTCTGTGAGCGCGGCACCATGTTTGGCTACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaccttgtttctcatgtgttctttcttacgcgtttgcgtttgtttgtctctagGTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAATCCAAACGTCATGGTCTGTGAGCGCGGCACCATGTTTGGCTACA
                        ttcttac  putative branch site (score: 6)
                                            tttgtctct  putative PPT
                       tttctta  TA-rich tract