RetrogeneDB ID: retro_cpor_993

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_381:130402..130728(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000012875
• Aliases: None
• Description: None

Sequence

>retro_cpor_993
TCTGCTGCTGTTGGCATTACCCCATTCAAATCGTCGACCACAAGACTGCATACTCTTATTTCCAATAAGAAACCAGTATT
TGATCTCAAAGCAAGTTTGTCTCATCCCCTCAACTATGAGTCACACAAAGGTAAGCTGAAACCATGGGTCAATTAAAAAA
ATAATTCTCTGAATTAACATGTAAGTAGAGTGAGTTTCCATCAGAAAACTTACAAGCAACCTCTGCTCCAAACCAGGGAA
GAGTAACAGAAGAAACACAAGCAAGAATAGAAGGAGAAGAAAGCTGAGGCTCTGGGAGCTCAAAAGGGCTCATTATTGTT
AAAGAT

Alignment

ORF - retro_cpor_993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 64.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NSAAGITPFNLTAKGMQTPVSSKKPVFDLKASLSRPLNYEPHKGKLKPWGQSKENNSLNEHVSRVSYHKK
          ..A.GITPF........T..S.KKPVFDLKASLS.PLNYE.HKGKLKPW...K.NNSLN.HVSRVS.H.K
Retrocopy SAAVGITPFKSSTTRLHTLISNKKPVFDLKASLSHPLNYESHKGKLKPWVN*K-NNSLN*HVSRVSFHQK

Parental  TYKQPPLHTREEQRKKHEQERKEKKAKVLEAR-RGLTVVKD
          TYKQP.L.TREE..KKH.QE.KEKKA..L.A...GL..VKD
Retrocopy TYKQPLLQTREE*QKKHKQE*KEKKAEALGAQ<KGLIIVKD

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	6.33 RPM
SRP017611_kidney	0.00 RPM	4.08 RPM
SRP017611_liver	0.00 RPM	1.83 RPM
SRP040447_lung	0.03 RPM	4.64 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.46 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_993 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_993 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.

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010774	1 retrocopy	retro_btau_1714,
Canis familiaris	ENSCAFG00000009538	3 retrocopies	retro_cfam_1685, retro_cfam_2137, retro_cfam_578,
Cavia porcellus	ENSCPOG00000012875	1 retrocopy	retro_cpor_993 ,
Myotis lucifugus	ENSMLUG00000009782	1 retrocopy	retro_mluc_389,
Mustela putorius furo	ENSMPUG00000008844	1 retrocopy	retro_mputfur_1626,
Otolemur garnettii	ENSOGAG00000034763	1 retrocopy	retro_ogar_3125,
Tupaia belangeri	ENSTBEG00000014283	1 retrocopy	retro_tbel_4088,