RetrogeneDB ID: retro_rnor_2052

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:39880097..39880371(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lyrm4
• Ensembl ID: ENSRNOG00000047970
• Aliases: None
• Description: LYR motif containing 4 [Source:MGI Symbol;Acc:MGI:2683538]

Sequence

>retro_rnor_2052
ATGGCAGCCTCCAGCTGTGCAAAAGTTTTAGAACTGTACCGGGCAATGATGAGAGAGAGCAAGCATTTCAGCGCCTACAA
TTACAGAATGTATGCTGTCAGGAGAATAAGAGATCCCTTCTGAGAAAATCAGAATGTAAAAGGCCCCATAGAAATACAAG
CCCTTGATGAATAAAGCCGAAAGAGACCTTGAACCAAACCGCAGACAGGTTCATATTGGCCAACCATACTCAACTGACAA
GCTTATCATTGAGAATCAAGAGAAGCCCAGGACA

Alignment

ORF - retro_rnor_2052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASSRAQVLDLYRAMMRESKHFSAYNYRMYAVRRIRDAFRENKNVKDPVEIQA-LVNKAKRDLEIIRRQ
          MAASS.A.VL.LYRAMMRESKHFSAYNYRMYAVRRIRD.F.EN.NVK.P.EIQA.L.NKA.RDLE..RRQ
Retrocopy MAASSCAKVLELYRAMMRESKHFSAYNYRMYAVRRIRDPF*ENQNVKGPIEIQA>LMNKAERDLEPNRRQ

Parental  VLIGQLYSTDKLIIENQENPRT
          V.IGQ.YSTDKLIIENQE.PRT
Retrocopy VHIGQPYSTDKLIIENQEKPRT

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	0.22 RPM	4.24 RPM
SRP017611_kidney	0.00 RPM	6.84 RPM
SRP017611_liver	0.00 RPM	2.15 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2052 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2052 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2052 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031432	1 retrocopy	retro_btau_783,
Callithrix jacchus	ENSCJAG00000021370	1 retrocopy	retro_cjac_1371,
Homo sapiens	ENSG00000214113	1 retrocopy	retro_hsap_194,
Macropus eugenii	ENSMEUG00000005958	1 retrocopy	retro_meug_656,
Myotis lucifugus	ENSMLUG00000028065	1 retrocopy	retro_mluc_394,
Mustela putorius furo	ENSMPUG00000000532	1 retrocopy	retro_mputfur_1459,
Mus musculus	ENSMUSG00000046573	1 retrocopy	retro_mmus_2374,
Nomascus leucogenys	ENSNLEG00000011472	1 retrocopy	retro_nleu_1002,
Rattus norvegicus	ENSRNOG00000047970	2 retrocopies	retro_rnor_1862, retro_rnor_2052 ,
Tursiops truncatus	ENSTTRG00000007073	1 retrocopy	retro_ttru_552,