RetrogeneDB ID: retro_rnor_2200

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:23842005..23842299(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ap4s1
• Ensembl ID: ENSRNOG00000005765
• Aliases: None
• Description: adaptor-related protein complex AP-4, sigma 1 [Source:RefSeq peptide;Acc:NP_001124471]

Sequence

>retro_rnor_2200
ATAAAGTTTTTCCTTGTAGTGAGCAAACAAGGGCAGACCCAACTGTCTAAGTACTATGAGCATGTAGACATTAATAAACA
TGCGCTTCTGGAAACCAAGGTCAGCAAGAGCTGCCTGTCTCAATCCAGTGAACAATGCTCTTGCATTGAATACATGGATT
TTAAGCTGATCTACGCAGCAATTCACAGCTCTCTTTGTTGTGGTTGGAGTTAATGACACTGAGAATGAGATGGCTATCTA
TGAATTCACCACAATTTTGTGGAAGTTTTAGATGAGTACCTCAGCAGAGTGAAC

Alignment

ORF - retro_rnor_2200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.0 %
• Parental protein coverage: 68.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IKFFLMVNRQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIY-RQYAALFVVVG
          IKFFL.V..QGQT.LSKYYEHVDINK.ALLET.VSKSCLS.SSEQCS.IEY.DFKLIY..Q..ALFVVVG
Retrocopy IKFFLVVSKQGQTQLSKYYEHVDINKHALLETKVSKSCLSQSSEQCSCIEYMDFKLIY>QQFTALFVVVG

Parental  VNDTENEMAIYEFI-HNFVEVLDEYFSRVS
          VNDTENEMAIYEF..HNFVEVLDEY.SRV.
Retrocopy VNDTENEMAIYEFT<HNFVEVLDEYLSRVN

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	9.85 RPM
SRP017611_kidney	0.00 RPM	8.44 RPM
SRP017611_liver	0.00 RPM	6.32 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2200 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2200 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000011671	1 retrocopy	retro_mluc_1841,
Macaca mulatta	ENSMMUG00000003123	1 retrocopy	retro_mmul_17,
Monodelphis domestica	ENSMODG00000017579	1 retrocopy	retro_mdom_1774,
Ornithorhynchus anatinus	ENSOANG00000014031	1 retrocopy	retro_oana_60,
Pongo abelii	ENSPPYG00000005723	1 retrocopy	retro_pabe_2889,
Rattus norvegicus	ENSRNOG00000005765	1 retrocopy	retro_rnor_2200 ,
Rattus norvegicus	ENSRNOG00000015865	2 retrocopies	retro_rnor_1030, retro_rnor_1516,