RetrogeneDB ID: retro_cpor_1043

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:49800153..49800660(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMAT5
• Ensembl ID: ENSCPOG00000020994
• Aliases: None
• Description: None

Sequence

>retro_cpor_1043
GGGAAGCGGTACTTCCGTGACGACTGTGACCGCCCTTTCAGGGATAACCTCCATAACCAGAAGAAGCACCCGAATAGGGT
ACAACACCAGAAGGCCAAGAAAATATGGAATAGCCATGTTCAGACAGGCAGTTGCCATCTTGCTGGATGAGATAAACAAA
AGGCTCTGCAGGAATTTCCTGTTGACAGGACAAGGTGACTTCTCTCCAATTGAAGATTTTCCCGTATGTCAGAGCAAGAC
TTGTAGGAGCTGAGCATCCAGGTGGAGGAGCAAAGCCAGGCCAGGGAGGGGCTGCTGGAATCCCCTGAGCTCCCTGAGGG
CTGTCTGGAAGACTGGCTGGAGGCCCGGGCCAAGATACCGAGCTTAGCCTCAAGCAGCAGGGTCAAAACCCTCAGAGCCA
CCATCTTCCAGTAACCTGTGGGCTGGCTGCCAGTCCAGGAGCTGCCCCATCCCTGCAGGTACCCTCACTGAGTGGCATAG
TGCCTGCAGCCCAGAGTGCAGTGGGGC

Alignment

ORF - retro_cpor_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.18 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKRYFCDYCDRSFQDNLHNRKKHLNGLQHLKAKKMWYD-MFRDAAAILLDEENKRPCRKFLLTGQCDFG-
          GKRYF.D.CDR.F.DNLHN.KKH.N..QH.KAKK.W...MFR.A.AILLDE.NKR.CR.FLLTGQ.DF..
Retrocopy GKRYFRDDCDRPFRDNLHNQKKHPNRVQHQKAKKIWNS>MFRQAVAILLDEINKRLCRNFLLTGQGDFS<

Parental  SNCRFSHMSEQDLQELSIQVEEERRAREWPLETPELPEGHLEDWLEKRAKRLSSAPSSRVEPLRATVFQY
          SN.RFS.MSEQDL.ELSIQVEE...ARE..LE.PELPEG.LEDWLE.RAK..S.A.SSRV..LRAT.FQ.
Retrocopy SN*RFSRMSEQDL*ELSIQVEEQSQAREGLLESPELPEGCLEDWLEARAKIPSLASSSRVKTLRATIFQ*

Parental  PVGWPPVQELPPSLRAPPPGGWPLQPRVQWG
          PVGW.PVQELP...R.P......LQPRVQWG
Retrocopy PVGWLPVQELPHPCRYPH*VA*CLQPRVQWG

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	11.85 RPM
SRP017611_kidney	0.00 RPM	10.89 RPM
SRP017611_liver	0.00 RPM	8.75 RPM
SRP040447_lung	0.00 RPM	13.09 RPM
SRP040447_skeletal_muscle	0.00 RPM	20.56 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1043 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1043 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008059	1 retrocopy	retro_amel_866,
Canis familiaris	ENSCAFG00000012343	2 retrocopies	retro_cfam_1130, retro_cfam_1424,
Cavia porcellus	ENSCPOG00000020994	1 retrocopy	retro_cpor_1043 ,
Echinops telfairi	ENSETEG00000003789	2 retrocopies	retro_etel_2098, retro_etel_421,
Felis catus	ENSFCAG00000004251	1 retrocopy	retro_fcat_824,
Myotis lucifugus	ENSMLUG00000017398	1 retrocopy	retro_mluc_568,
Mustela putorius furo	ENSMPUG00000013253	1 retrocopy	retro_mputfur_875,