RetrogeneDB ID: retro_cpor_129

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:23943376..23943730(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOP16
• Ensembl ID: ENSCPOG00000026072
• Aliases: None
• Description: None

Sequence

>retro_cpor_129
AATGCACCATGGAAGGCAGCGCCATGGATTAAGTGTTCCCCCGACATCCAACACGCCTGGGACCATGCCAGATCCATGCA
GCAGAACCTGGCAGAGATAAAGTTAGCCTTAGACCTCAACAAAGGGGTTCCCCTCCATCAAAGAAAGATGTAAAGGTCAT
GGAGGTAGACATGGAGTACAGGCCCAAGGAGTTTTTGTAGAAGCACTATATTCTAAATGACCTCGAGGCAGAAGCCAAGC
TTCTAGAAAAAGAAACACCTTGCCCCAGGACCTTATTGGCTGCATACACTACCACATGGTAGCAAACATGGAGAGGATTA
CAAGGGCATGGGCTGGCATGAGAATAATGACTAT

Alignment

ORF - retro_cpor_129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.46 %
• Parental protein coverage: 65.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NARRKAAPRIQCS-HIRHAWDHTKSVRQNLAEMGL-AMDPN-KAVPVRKRKVKAMEVDVEERPKELVRKP
          NA..KAAP.I.CS..I.HAWDH..S..QNLAE..L....P.....P..K..VK.MEVD.E.RPKE...K.
Retrocopy NAPWKAAPWIKCSPDIQHAWDHARSMQQNLAEIKL<SLRPQQRGSPPSKKDVKVMEVDMEYRPKEFL*KH

Parental  YVLNDLEAEASLPEKKGNTLSRDLIEYV-HHMVEN-YGEDYKAMARDEKNYY
          Y.LNDLEAEA.L.EK........L..Y...HMV.N..GEDYK.M...E.N.Y
Retrocopy YILNDLEAEAKLLEKETPCPRTLLAAYT<YHMVAN<HGEDYKGMGWHENNDY

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	5.75 RPM
SRP017611_kidney	0.00 RPM	15.70 RPM
SRP017611_liver	0.00 RPM	16.02 RPM
SRP040447_lung	0.00 RPM	13.34 RPM
SRP040447_skeletal_muscle	0.00 RPM	21.71 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_129 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_129 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012315	1 retrocopy	retro_cjac_2208,
Cavia porcellus	ENSCPOG00000026072	1 retrocopy	retro_cpor_129 ,
Echinops telfairi	ENSETEG00000010391	1 retrocopy	retro_etel_1329,
Myotis lucifugus	ENSMLUG00000003504	1 retrocopy	retro_mluc_2425,
Mustela putorius furo	ENSMPUG00000012552	1 retrocopy	retro_mputfur_381,
Mus musculus	ENSMUSG00000025869	2 retrocopies	retro_mmus_3033, retro_mmus_3258,
Rattus norvegicus	ENSRNOG00000017284	1 retrocopy	retro_rnor_2739,
Sus scrofa	ENSSSCG00000029577	1 retrocopy	retro_sscr_510,