RetrogeneDB ID: retro_rnor_2380

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:90576496..90577051(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000005471
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Akr1b8
• Ensembl ID: ENSRNOG00000009734
• Aliases: None
• Description: aldose reductase-related protein 2 [Source:RefSeq peptide;Acc:NP_775159]

Sequence

>retro_rnor_2380
GAGGACCTCTTCATTGTCAGCAAGTTGTGGCTCACCTGCTTTGAGAAAAAACTGCTAAAGGAAGCCTTTCAGAAGACCCT
CATGGATCTCAAGCTCGACTATTTGGACCTCTATCTTATTCACTGGCCACAGGGACTTCAGCCGAGAAAGGAGTTATTCC
CCAAAGAGGATCAAGGCAGTATCCTTACCAATAAAACAACATTGTTGGAAGCCTGGGAGGGCATGAAGGAACTGGTGGAC
CAGGGACTGTCGAAAACTCTGGGCGTCTCCAACTTCAGTCACTTCCAGATCGAAAGGCTCCTGAACAAGCCTGGACTGAA
ACATAAGCCAGTGACCAACCAGGTTGAGTGCCACCCTAACCTCACCCAGGAAAAACTGACCCAATACTGTCACTCCAAGG
GCATCACAGTCACAGCATACAGTCCCCTGGGCTCCCCAGACAGGCCTAGCGCCAAGCCAGAGGACCCTTCACTATTAAAG
TACCCCAAAATTAAAGAGATTGCCGCCAAGCACAAGAAAACTATACCCCAGGTTCTGATTCGGTTCCACATCCAG

Alignment

ORF - retro_rnor_2380 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 58.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDLFIVSKLWPTCFEKKLLKEAFQKTLTDLKLDYLDLYLIHWPQGFQAGKELFPKDEQGNVLPSKTTFLE
          EDLFIVSKLW.TCFEKKLLKEAFQKTL.DLKLDYLDLYLIHWPQG.Q..KELFPK..QG..L..KTT.LE
Retrocopy EDLFIVSKLWLTCFEKKLLKEAFQKTLMDLKLDYLDLYLIHWPQGLQPRKELFPKEDQGSILTNKTTLLE

Parental  AWEGMEELVDQGLVKALGVSNFNHFQIERLLNKPGLKHKPVTNQVECHPYLTQEKLIQYCHSKGIVVTAY
          AWEGM.ELVDQGL.K.LGVSNF.HFQIERLLNKPGLKHKPVTNQVECHP.LTQEKL.QYCHSKGI.VTAY
Retrocopy AWEGMKELVDQGLSKTLGVSNFSHFQIERLLNKPGLKHKPVTNQVECHPNLTQEKLTQYCHSKGITVTAY

Parental  SPLGSPDRPRAKPDDPSLLQDPKIKEIAAKHKKTTAQVLIRFHIQ
          SPLGSPDRP.AKP.DPSLL..PKIKEIAAKHKKT..QVLIRFHIQ
Retrocopy SPLGSPDRPSAKPEDPSLLKYPKIKEIAAKHKKTIPQVLIRFHIQ

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	0.07 RPM	0.29 RPM
SRP017611_kidney	0.07 RPM	10.54 RPM
SRP017611_liver	0.00 RPM	3.16 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2380 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2380 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
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,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,