RetrogeneDB ID: retro_rnor_2702

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:92746901..92747228(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000022614
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Srp14
• Ensembl ID: ENSRNOG00000007512
• Aliases: None
• Description: signal recognition particle 14 kDa protein [Source:RefSeq peptide;Acc:NP_001099967]

Sequence

>retro_rnor_2702
ATGGTGTTGCTCAAGAGCGAGCAGTTCCTGACGAAGCTGACCAGGCTCTTCCAGAAGTGCTGGTCGTCGGGTAGCGTGTT
TATCACCCTGAAGAAGTGTGATGGTTGCACCAAACCCATCCCACAGAAGAGTTCCGTGGAGGGCCTCGAGCCCGCAGAAA
ACAAGTGTCTGTTAAGGGCCACGGATGGGAAAAGGAAGATCAGCACAGTGGGGAGCTCCAAAGAAGAGAATAAGTTTGAG
ATGGCCTATTCAAATCTACTGAGAGCCGACATGAATGGGCTGAAGAAGAGGGACAAGAAGAACAAGAGTAAGAAGAGCAA
ACCAGCA

Alignment

ORF - retro_rnor_2702 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.91 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLLESEQFLTELTRLFQKCRSSGSVFITLKKYDGRTKPIPRKSSVEGLEPAENKCLLRATDGKRKISTV
          MVLL.SEQFLT.LTRLFQKC.SSGSVFITLKK.DG.TKPIP.KSSVEGLEPAENKCLLRATDGKRKISTV
Retrocopy MVLLKSEQFLTKLTRLFQKCWSSGSVFITLKKCDGCTKPIPQKSSVEGLEPAENKCLLRATDGKRKISTV

Parental  VSSKEVNKFQMAYSNLLRANMDGLKKRDKKNKSKKSKPA
          .SSKE.NKF.MAYSNLLRA.M.GLKKRDKKNKSKKSKPA
Retrocopy GSSKEENKFEMAYSNLLRADMNGLKKRDKKNKSKKSKPA

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	0.14 RPM	36.52 RPM
SRP017611_kidney	0.07 RPM	34.05 RPM
SRP017611_liver	0.07 RPM	23.06 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2702 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2702 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2702 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017231	1 retrocopy	retro_amel_1566,
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Erinaceus europaeus	ENSEEUG00000012759	1 retrocopy	retro_eeur_357,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Myotis lucifugus	ENSMLUG00000010531	5 retrocopies	retro_mluc_1489, retro_mluc_2284, retro_mluc_2545, retro_mluc_375, retro_mluc_384,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Mustela putorius furo	ENSMPUG00000008324	1 retrocopy	retro_mputfur_376,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Ochotona princeps	ENSOPRG00000008599	1 retrocopy	retro_opri_619,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Rattus norvegicus	ENSRNOG00000007512	1 retrocopy	retro_rnor_2702 ,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,