RetrogeneDB ID: retro_cpor_877

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_30:7580525..7581089(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRRF
• Ensembl ID: ENSCPOG00000007351
• Aliases: None
• Description: mitochondrial ribosome recycling factor [Source:HGNC Symbol;Acc:7234]

Sequence

>retro_cpor_877
GTCTTGATCAGACCTGGTTCAGAAACTGCACTAAAGACAGTGAGTGGAAAATGAGTCTGATGATAGCCAACACATGGCTT
ATCAGGCTGTACCAGTTCACCATTGTGCAACCGAGAAAGCCGAAGCCAAACAGAAAGGACAATGCCAAACCAGAGTAAAC
TAACATGGCTTTGGCTGAAGATGTAATCCACTTGGAATAGATGGATGAGGAAAGGAAGACTGTGATAGAAGTACTCAAGG
ATAATTTCAGTAAGACTCTCAATATAAGGACTTTACTAGGATCCCTTGATCTTCTTACTGTGGTGACTGTTGATGGAAAG
CTTGCTTTAAACCAGATTGGCCAGATCACCATAAAGTCGCTGCAGTTGATTTTGGTGAAATATGGCCAGCTTCCCAAAGT
GTACAGCCGCAGCTAACAAAGCTATGAGAGAAAGCAGAATGAGTCTGAACCCAGTGCAAACGACACTAATTCGGGTAACC
AGGGAGCACAGGGAGATGCTGGAGAGACTGGCTGAACAGAATATCAAGCAGGTCAAAGACTTTACAGTTCGTAAAGATGC
AATG

Alignment

ORF - retro_cpor_877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.81 %
• Parental protein coverage: 74.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLIRPVSEIALKTVSGK-QPDHSQHMAYQAVPVRHFAT-KKTKAKGKGQSQARVNINTALVEDIINLEKV
          VLIRP.SE.ALKTVSGK...D.SQHMAYQAVPV.H.AT..K.K...K.........N.AL.ED.I.LE..
Retrocopy VLIRPGSETALKTVSGK>ESDDSQHMAYQAVPVHHCAT>RKPKPNRKDNAKPE*T-NMALAEDVIHLE*M

Parental  DEEMKSVIELLKDNFNKTLNIRTSPGSLDHITVVTADGKLALNQISQISMKSPQLILV-NMASFPECTAA
          DEE.K.VIE.LKDNF.KTLNIRT..GSLD..TVVT.DGKLALNQI.QI..KS.QLILV.NMASFP.CTAA
Retrocopy DEERKTVIEVLKDNFSKTLNIRTLLGSLDLLTVVTVDGKLALNQIGQITIKSLQLILV>NMASFPKCTAA

Parental  AIKAIRESGMNLNPEVEGTLIRVPIPKVTREHREMLVKLAKQNTNKAKDSLRRVRADAM
          A.KA.RES.M.LNP.V..TLIRV......RE..E.L.....QN....KD....VR.DAM
Retrocopy ANKAMRESRMSLNP-VQTTLIRV--TREHREMLERLAE---QNIKQVKDF--TVRKDAM

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	8.17 RPM
SRP017611_kidney	0.00 RPM	15.49 RPM
SRP017611_liver	0.00 RPM	7.79 RPM
SRP040447_lung	0.03 RPM	6.53 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.86 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_877 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_877 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007351	1 retrocopy	retro_cpor_877 ,
Homo sapiens	ENSG00000148187	1 retrocopy	retro_hsap_4897,
Gorilla gorilla	ENSGGOG00000023499	1 retrocopy	retro_ggor_98,
Mus musculus	ENSMUSG00000026887	1 retrocopy	retro_mmus_340,
Nomascus leucogenys	ENSNLEG00000017177	1 retrocopy	retro_nleu_1263,
Pongo abelii	ENSPPYG00000019570	1 retrocopy	retro_pabe_80,
Pan troglodytes	ENSPTRG00000021324	1 retrocopy	retro_ptro_3265,
Rattus norvegicus	ENSRNOG00000025997	2 retrocopies	retro_rnor_1477, retro_rnor_2654,
Sarcophilus harrisii	ENSSHAG00000012469	2 retrocopies	retro_shar_610, retro_shar_704,
Tupaia belangeri	ENSTBEG00000016569	1 retrocopy	retro_tbel_4411,