RetrogeneDB ID: retro_rnor_2559

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:32792126..32792622(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Akr1d1
• Ensembl ID: ENSRNOG00000013004
• Aliases: None
• Description: 3-oxo-5-beta-steroid 4-dehydrogenase [Source:RefSeq peptide;Acc:NP_620239]

Sequence

>retro_rnor_2559
ATTAACCTCAGTGCCGAGAACCACCAAATACCTCTAGAATGCTAGAAACAGCTTTCTAGTCATTGGGCGTGACACCTACT
CAGATCGTAAACCTATTCCTACAGAGGCCTTCTACCTCTGTGAAAGTGGTCATTGACACCAGGTATTGACACCCCAGTAG
GGATGGCTTCCACCACAATGAACATGAAGTTAGTGAGGACATCAGAGAGATGATAGGAGAAGGGAAGGTAAGGAGGGAAG
AGATTTTCTACTGAGTCGAGATGTGAGCTACAAATCATGTCCTGGAGATGGTCTGCCCATTCCTGCAGAGGATATTGGTG
ACCCTCAAGCTAGGTTATAGAGATGTTTACATCAGTGAGATACCCATGGCCTTTCAGCTAGGAAGAAATTTGATCTTGGA
GATGAAAATGACAAATGGTTACATCATGACTTGAATATGTGCAGTACTGACAAAGCCCTGGAAGATTGCAAAGATGTTGG
CTTGGTGAAACTCCTA

Alignment

ORF - retro_rnor_2559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.79 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNLSTANHHIPL-NDGNSIPIIGLGTYSDPRPVPGKTFI-AVKTAIDEGYRHIDGAYVYRNEHEVGEAIR
          .NLS..NH.IPL.N..NS...IG..TYSD..P.P...F...VK..ID..Y.H........NEHEV.E.IR
Retrocopy INLSAENHQIPL>NARNSFLVIGRDTYSDRKPIPTEAFY>SVKVVIDTRY*HPSRDGFHHNEHEVSEDIR

Parental  EKVAEGKVKREEIFYCGKLWSTDHDPEMVRPALERTLQTLKLDYIDLYIIEMPMAFKPG-EEFYPKDENG
          E...EGKV.REEIFY......T.H..EMV.P.L.R.L.TLKL.Y.D.YI.E.PMAF..G...F...DEN.
Retrocopy EMIGEGKVRREEIFY*VEM*ATNHVLEMVCPFLQRILVTLKLGYRDVYISEIPMAFQLG<KKFDLGDEND

Parental  RVIYHKSNLCATWEALEACKDAGLVKSL
          ....H..N.C.T..ALE.CKD.GLVK.L
Retrocopy KWLHHDLNMCSTDKALEDCKDVGLVKLL

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	0.22 RPM
SRP017611_kidney	0.00 RPM	0.35 RPM
SRP017611_liver	0.00 RPM	719.17 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2559 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2559 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012872	1 retrocopy	retro_cjac_1688,
Homo sapiens	ENSG00000122787	1 retrocopy	retro_hsap_257,
Gorilla gorilla	ENSGGOG00000014684	1 retrocopy	retro_ggor_307,
Nomascus leucogenys	ENSNLEG00000013710	1 retrocopy	retro_nleu_860,
Pongo abelii	ENSPPYG00000018037	1 retrocopy	retro_pabe_406,
Pan troglodytes	ENSPTRG00000019740	1 retrocopy	retro_ptro_217,
Rattus norvegicus	ENSRNOG00000009513	1 retrocopy	retro_rnor_1438,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Rattus norvegicus	ENSRNOG00000013004	1 retrocopy	retro_rnor_2559 ,
Rattus norvegicus	ENSRNOG00000017165	1 retrocopy	retro_rnor_1441,
Rattus norvegicus	ENSRNOG00000038361	1 retrocopy	retro_rnor_2046,