RetrogeneDB ID: retro_rnor_1325

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:87662236..87662923(-)
• Located in intron of: ENSRNOG00000016716

Retrocopy information

• Ensembl ID: ENSRNOG00000016710
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam64a
• Ensembl ID: ENSRNOG00000008040
• Aliases: Fam64a, RGD1308747
• Description: protein FAM64A [Source:RefSeq peptide;Acc:NP_001107253]

Sequence

>retro_rnor_1325
ATGGCGTCTCAGTGGCAGGGCATGAGGACCTCCGTGCGCAGACGATCACTCCTAAAGGAGGAACAGCTAGAGAAGGAGGT
GACCCGGTCTGCTGGAGGTCATCTGGAGACCGGTCCCTTGGGATCCATGTGCAGACAGTTCCATAGGAGGCTGCCACTGA
GATCGGTCAGCATGAACCGCGGTAATGGCCCCTCCTGGAAACGCCTGGAAACCCCAGAGCCAGAGCAGCAAGGTCTTCAG
GCTGCAGCTCGCTCAGCCAAAAGCGCCTTGGGTGCCATGTCCCAGAGGATCCAGGAGTCCTGTCAAAGTGACACCAAGTG
GTTGATGGAGACCCAGGTGAGAGTGAGGAGGAATCGAGGAGCCCAGAAAGACAGAGGATCGCCATCACCCAGTCTGAGTC
AGAAGAACACTCAGCTATGCAGAGCCAACCGGGATGCTAGAGAGCGAGGACATCCTCGCCTCTCTGGCCAGATGGGTCCA
CATGCCCATCGCCGTCAGCGGCTAAGGAGAGAGGCTGCCCTCCGGAGCCCCTGTTCCTCCACAGATCCTCTCTACTCTCC
CAGTGAGTCTGACAGCGACCTAGAGCCTATGGGAGCTGGAATCCAGCATCTTCAGCTGTCTCAAAAGCTGGACAAAGCCA
TCAAGGCTGAAGAGAGCAGTGACATGATCATCTCCCTTATCCGTGAA

Alignment

ORF - retro_rnor_1325 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.3 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASQWQGMRTSVRRRSLLKEEQLEKEVTRSAGGHLETGPLGSLCRQFQRRLPLRAVSLNLGNGPSWKRLE
          MASQWQGMRTSVRRRSLLKEEQLEKEVTRSAGGHLETGPLGS.CRQF.RRLPLR.VS.N.GNGPSWKRLE
Retrocopy MASQWQGMRTSVRRRSLLKEEQLEKEVTRSAGGHLETGPLGSMCRQFHRRLPLRSVSMNRGNGPSWKRLE

Parental  TPEPEQQGLQAAARSAKSALGAMSQRIQESCQSGTKWLMETQVRVRRKRGAQKDRGSPPPSLSPKNTRLC
          TPEPEQQGLQAAARSAKSALGAMSQRIQESCQS.TKWLMETQVRVRR.RGAQKDRGSP.PSLS.KNT.LC
Retrocopy TPEPEQQGLQAAARSAKSALGAMSQRIQESCQSDTKWLMETQVRVRRNRGAQKDRGSPSPSLSQKNTQLC

Parental  RANRDARGGGLPRLSGQMGPHAHRRQRLRREAALRSPCSSTDPLCSPSESDSDLEPVGAGIQHLQKLSQK
          RANRDAR..G.PRLSGQMGPHAHRRQRLRREAALRSPCSSTDPL.SPSESDSDLEP.GAGIQHLQ.LSQK
Retrocopy RANRDARERGHPRLSGQMGPHAHRRQRLRREAALRSPCSSTDPLYSPSESDSDLEPMGAGIQHLQ-LSQK

Parental  LDKAIKAEESGDMTVSLISE
          LDKAIKAEES.DM..SLI.E
Retrocopy LDKAIKAEESSDMIISLIRE

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	0.43 RPM
SRP017611_kidney	0.00 RPM	0.14 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1325 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1325 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006997	1 retrocopy	retro_amel_1136,
Homo sapiens	ENSG00000129195	3 retrocopies	retro_hsap_2371, retro_hsap_3030, retro_hsap_3071,
Gorilla gorilla	ENSGGOG00000012309	3 retrocopies	retro_ggor_1801, retro_ggor_2091, retro_ggor_2109,
Macaca mulatta	ENSMMUG00000017760	3 retrocopies	retro_mmul_1778, retro_mmul_1935, retro_mmul_959,
Mus musculus	ENSMUSG00000020808	1 retrocopy	retro_mmus_3385,
Nomascus leucogenys	ENSNLEG00000009164	3 retrocopies	retro_nleu_361, retro_nleu_725, retro_nleu_843,
Otolemur garnettii	ENSOGAG00000027433	1 retrocopy	retro_ogar_1490,
Pongo abelii	ENSPPYG00000007877	3 retrocopies	retro_pabe_2141, retro_pabe_2509, retro_pabe_2545,
Pan troglodytes	ENSPTRG00000008641	3 retrocopies	retro_ptro_1734, retro_ptro_2044, retro_ptro_2070,
Rattus norvegicus	ENSRNOG00000008040	1 retrocopy	retro_rnor_1325 ,