RetrogeneDB ID: retro_cfam_1776

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:1138698..1139114(+)
• Located in intron of: ENSCAFG00000010773

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL1
• Ensembl ID: ENSCAFG00000014364
• Aliases: None
• Description: GrpE-like 1, mitochondrial (E. coli) [Source:HGNC Symbol;Acc:19696]

Sequence

>retro_cfam_1776
CCTCTCCTGTTGTGTACAGCTGAAAAACAAAAGAACAGTGGCTAGAATGGAAGAGAGGACATGGGTCAAAATAGAACAGA
AGAGAGATACTTCCTCTACAGAGAAGATACTTATGGCAGAGAAGGTCAAGTTAGAAGAGCAACTAGAAGAGCCTATGGAA
AAATAAAAGTGAGGTTTGACAGATACCAAGAACTTCCTGCAGAGGAGCCGAAAATGGTGGAGGAGGCAAAATTATATGAT
ATTTAGGAAATCTGCAAGGACTTGCTAGACGTTGCAGGTATTTTGGAGAAAGCAACACAATGTGTGCAAAAGAAGAAATT
AAAGATGACAACCCTGTAAACCTGTAGAAAAGCCTCATATTGACTGAAGTCCGCATTCAGAAGGTGTTCAGAAAGCACAG
CTTACTCGAATTGAGC

Alignment

ORF - retro_cfam_1776 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 60.87 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PRLLCTATKQKN-GRNLEEDVGQN-EQKTDTPSTEKTLMDEKVKLEEQLKETVEKYKRALADTENLRQRS
          P.LLCTA.KQKN.G.N..ED.GQN.EQK.DT.STEK.LM.EKVKLEEQL.E..EK.K..L.DT.N..QRS
Retrocopy PLLLCTAEKQKNSG*NGREDMGQN>EQKRDTSSTEKILMAEKVKLEEQLEEPMEK*K*GLTDTKNFLQRS

Parental  Q-KLVEEAKLYGIQGFCKDLLEVADILEKATQSV-PKEEVKDDNPHLKNLYEGLVMTEVQIQKVFTKHGL
          ..K.VEEAKLY.I...CKDLL.VA.ILEKATQ.V..KEE.KDDNP...NL...L..TEV.IQKVF.KH.L
Retrocopy R<KMVEEAKLYDI*EICKDLLDVAGILEKATQCV<AKEEIKDDNP--VNL*KSLILTEVRIQKVFRKHSL

Parental  LRLN
          L.L.
Retrocopy LELS

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
SRP012049_cerebellum	0.04 RPM	21.80 RPM
SRP017611_brain	0.00 RPM	21.83 RPM
SRP017611_kidney	0.00 RPM	81.75 RPM
SRP017611_liver	0.00 RPM	26.25 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1776 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1776 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1776 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014364	1 retrocopy	retro_cfam_1776 ,
Homo sapiens	ENSG00000109519	3 retrocopies	retro_hsap_3746, retro_hsap_3864, retro_hsap_3870,
Loxodonta africana	ENSLAFG00000002590	1 retrocopy	retro_lafr_535,
Monodelphis domestica	ENSMODG00000002955	1 retrocopy	retro_mdom_28,
Mustela putorius furo	ENSMPUG00000010471	1 retrocopy	retro_mputfur_32,
Nomascus leucogenys	ENSNLEG00000011822	1 retrocopy	retro_nleu_2642,
Otolemur garnettii	ENSOGAG00000032291	1 retrocopy	retro_ogar_1765,
Procavia capensis	ENSPCAG00000011314	1 retrocopy	retro_pcap_388,
Pongo abelii	ENSPPYG00000014573	1 retrocopy	retro_pabe_3235,
Pan troglodytes	ENSPTRG00000015894	3 retrocopies	retro_ptro_2544, retro_ptro_2633, retro_ptro_2636,
Sarcophilus harrisii	ENSSHAG00000007667	1 retrocopy	retro_shar_766,