RetrogeneDB ID: retro_cpor_451

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:16889164..16889434(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFB2M
• Ensembl ID: ENSCPOG00000013225
• Aliases: None
• Description: None

Sequence

>retro_cpor_451
AAGGCCTTGCTAGAAACGAGTGCCACAGTGATTGCACTTGAAAGCCACAAAAAAGTTTATTCCACATTTGAAGTCCTTAG
GGGAAAGGCTGAAAGGAAAACTAGAAGTGATCCAATGTGACTTTTTAAAAATGGATCTTAGCAATCGTAATTTAGTAAGA
CCACCCATTGTGCTTTCATGAGGACTTTTTCCAAGTTTGAGAATAAAAGCAAATTGTTGGTCAGAAGATACTCCTTTTAA
AGTAGTCATAATCTCCCTGTGAATTATGAA

Alignment

ORF - retro_cpor_451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.3 %
• Parental protein coverage: 56.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KALLETGASVIALESQKN-FIPHLKSLDEKRNGKLKVVHCDFFKMDPSNCNTVKPPIMLSQELFPTLGIK
          KALLET.A.VIALES.K..FIPHLKSL.E...GKL.V..CDF.KMD.SN.N.V.PPI.LS..LFP.L.IK
Retrocopy KALLETSATVIALESHKK>FIPHLKSLGERLKGKLEVIQCDFLKMDLSNRNLVRPPIVLS*GLFPSLRIK

Parental  ANSWLEDTPFKIVGM-FPINNE
          AN.W.EDTPFK.V....P.N.E
Retrocopy ANCWSEDTPFKVVII<LPVNYE

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	2.36 RPM
SRP017611_kidney	0.00 RPM	5.44 RPM
SRP017611_liver	0.00 RPM	2.92 RPM
SRP040447_lung	0.00 RPM	1.74 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.86 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_451 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_451 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	ENSCPOG00000013225	1 retrocopy	retro_cpor_451 ,
Homo sapiens	ENSG00000162851	1 retrocopy	retro_hsap_3548,
Gorilla gorilla	ENSGGOG00000001095	1 retrocopy	retro_ggor_2396,
Myotis lucifugus	ENSMLUG00000003923	1 retrocopy	retro_mluc_1302,
Macaca mulatta	ENSMMUG00000022915	1 retrocopy	retro_mmul_1814,
Nomascus leucogenys	ENSNLEG00000004146	1 retrocopy	retro_nleu_2323,
Oryctolagus cuniculus	ENSOCUG00000013727	2 retrocopies	retro_ocun_1557, retro_ocun_236,
Otolemur garnettii	ENSOGAG00000007823	2 retrocopies	retro_ogar_1444, retro_ogar_2187,
Pongo abelii	ENSPPYG00000000046	1 retrocopy	retro_pabe_3039,
Pan troglodytes	ENSPTRG00000002188	1 retrocopy	retro_ptro_2412,