RetrogeneDB ID: retro_sara_448

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_211486:61..373(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PCGF1
• Ensembl ID: ENSSARG00000007319
• Aliases: None
• Description: polycomb group ring finger 1 [Source:HGNC Symbol;Acc:17615]

Sequence

>retro_sara_448
GACGAGGAGGAGCGTCTGATTAATCTCTCTGAGCTGACCCAGTACATCTTGTGTTCCATTTGCAAAGGTTACTTGATAGA
TGCGACCACCATTACAGAATGTCTTCATACCTTTTGTAAAAGCTGCATTGTAAGACATTTTTACTATAGCAACAGATGTC
CAAAATGCAACATAGTAGTCCATCAGACTCAACCTCTTTATAACATAAGGTTGGACCGACAGTTACAAGACATAGTGTAC
AAATTAGTGATCAATCTAGAGGAAAGAGAAAAAAAGCAAATGCATGATTTCTATAAAGAAAGAGGTCTAGAA

Alignment

ORF - retro_sara_448 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.81 %
• Parental protein coverage: 80.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NEEDVRVKIKDLNEHIVCCLCAGYFVDATTITECLHTFCKSCIVKYLQTSKYCPMCNIKIHETQPLLNLK
          .EE........L...I.C..C.GY..DATTITECLHTFCKSCIV.....S..CP.CNI..H.TQPL.N..
Retrocopy DEEERLINLSELTQYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIR

Parental  LDRVMQDIVYKLVPGLQDSEEKRIREFYQSRGLD
          LDR..QDIVYKLV..L...E.K....FY..RGL.
Retrocopy LDRQLQDIVYKLVINLEEREKKQMHDFYKERGLE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_448 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000115289	1 retrocopy	retro_hsap_1029,
Mus musculus	ENSMUSG00000069678	1 retrocopy	retro_mmus_2722,
Nomascus leucogenys	ENSNLEG00000000752	1 retrocopy	retro_nleu_907,
Pongo abelii	ENSPPYG00000012270	1 retrocopy	retro_pabe_862,
Pan troglodytes	ENSPTRG00000012094	1 retrocopy	retro_ptro_704,
Sorex araneus	ENSSARG00000007319	1 retrocopy	retro_sara_448 ,
Sus scrofa	ENSSSCG00000008277	1 retrocopy	retro_sscr_1069,