RetrogeneDB ID: retro_sara_381

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_187844:4102..4660(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKRA
• Ensembl ID: ENSSARG00000003080
• Aliases: None
• Description: protein kinase, interferon-inducible double stranded RNA dependent activator [Source:HGNC Symbol;Acc:9438]

Sequence

>retro_sara_381
GAAGACGGGGAGACGTTCAGTTCGGACAAGATGATTACAGCTAAACCGGGGAAAATCCCCATTCAAGTCTTACACGAATA
TGGCATGAAGACCAAGAACATCCGGGTTTATGAGTGCTAAAGGTCCGATGTGTAGATACACGTGCCCACATTCACCTTCA
GAGTCGCAGTGGGTGACATAACTGCACAGGTGAAGGTACAAGTAAGAAGTTAGAGAAAGCTAGAGCTGCAGAGGCTGCCA
TAAACATTTTGAAAACCAGTGCAAGTATTTGTTTTGCAGCTCCTGATCCCTTAATGCCTGACCCTTCCCAGCAACCCAAG
AACCAGCTTAATCCCATTGGGTCAATACAGGAATTGGCAATTCATCATGGTTGGAGGTTTCCTGAACACACACTTTCCCA
GGAGGGAGGACCTGCTCATAAGAGGGAATATACCATAATTTGCAGACTAGAGTCATATATGGAAACTGGAAAAGGGGCAT
GCAAAAAAGCAAGCCAAGAGGACTTCTGCTGAGAAATTCCTTGCTAAATTCAGTACTATTTCTCCAGAGAATCACTTT

Alignment

ORF - retro_sara_381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.36 %
• Parental protein coverage: 59.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDGETFSSGKMITAKPGKTPIQVLHEYGMKTKNIPVYECERSDVQIHVPTFTFRVT-GDIT-CTGEGTSK
          EDGETFSS.KMITAKPGK.PIQVLHEYGMKTKNI.VYEC.RSDV.IHVPTFTFRV..GDIT.CTGEGTSK
Retrocopy EDGETFSSDKMITAKPGKIPIQVLHEYGMKTKNIRVYEC*RSDV*IHVPTFTFRVAVGDIT<CTGEGTSK

Parental  KLAKHRAAEAAINILKASASICFAAPDPLMPDPSKQPKNQLNPIGSLQELAIHHGWRLPEYTLSQEGGPA
          KL.K.RAAEAAINILK.SASICFAAPDPLMPDPS.QPKNQLNPIGS.QELAIHHGWR.PE.TLSQEGGPA
Retrocopy KLEKARAAEAAINILKTSASICFAAPDPLMPDPSQQPKNQLNPIGSIQELAIHHGWRFPEHTLSQEGGPA

Parental  HKREYTTICRLESYMETGKGA-SKKQAKRNAAEKFLAKFSTISPENHF
          HKREYT.ICRLESYMETGKGA..KKQAKR..AEKFLAKFSTISPENHF
Retrocopy HKREYTIICRLESYMETGKGA>AKKQAKRTSAEKFLAKFSTISPENHF

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_381 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 5 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000002185	1 retrocopy	retro_mmul_809,
Oryctolagus cuniculus	ENSOCUG00000005489	1 retrocopy	retro_ocun_1117,
Sorex araneus	ENSSARG00000003080	1 retrocopy	retro_sara_381 ,
Tursiops truncatus	ENSTTRG00000009700	1 retrocopy	retro_ttru_1852,