RetrogeneDB ID: retro_cpor_1225

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_59:874898..875405(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA1
• Ensembl ID: ENSCPOG00000025598
• Aliases: None
• Description: None

Sequence

>retro_cpor_1225
CACAGGCTGGACAATATGACCAAGGAGGCTGCGTCAGCTGGGGAGAATCACCTTAAAGTTATATTGACCTCAGTTGTGTC
TAGAAGGAAAGCCAATCGGTTACGAGATGGGCATTTTAAATATGCCTTTGGGAGTAATGTCATCCCACAGCCTTACCTGA
AGAATAGTGTGGTAGCTTACAACAACTTAATAGAAAACTCTCTAGCCTTTGTTGCTCCTTTTGCCAGTCAGAATCCATCT
TCTCATCCACTCCCTGATGATGCTGAGCAGCAGGCTGTGCTCTTAATGGCTTGCTTTGGGGGCACACTGCCTGCATCTCT
GCCTTCAGTGAACATGCATGACCTTTTTGAAGTTTTGCAGGTACACAGGGAAGTCATTCCTACACATACTGTTTATGCCC
TTAACATTGAAAGCCTTATCATGAAACTTTAGCACCCCAGTCACAAAGATCTGCAGCAAGACAAAACCCACTGCCAGCAT
TTGGCAGCCAAGGAAGAGATTTTGCTC

Alignment

ORF - retro_cpor_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.35 %
• Parental protein coverage: 55.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HGLDNVTEEAVSAVVYAVENHLKDILTSVVSRRKAYRLRDGHFKYAFGSNVIPQPYLKNSVVAYNNLIEN
          H.LDN.T.EA.S....A.ENHLK.ILTSVVSRRKA.RLRDGHFKYAFGSNVIPQPYLKNSVVAYNNLIEN
Retrocopy HRLDNMTKEAAS----AGENHLKVILTSVVSRRKANRLRDGHFKYAFGSNVIPQPYLKNSVVAYNNLIEN

Parental  PPAFSAPFAGQNPSSHPPPDDAEQQAALLLACSGDTLPASLPPVNMYDLFEALQVHREVIPTHTVYALNI
          ..AF.APFA.QNPSSHP.PDDAEQQA.LL.AC.G.TLPASLP.VNM.DLFE.LQVHREVIPTHTVYALNI
Retrocopy SLAFVAPFASQNPSSHPLPDDAEQQAVLLMACFGGTLPASLPSVNMHDLFEVLQVHREVIPTHTVYALNI

Parental  ERIIMKLWHPNHEELQQDKIHRQRLAAKEGLLL
          E..IMKL.HP.H..LQQDK.H.Q.LAAKE..LL
Retrocopy ESLIMKL*HPSHKDLQQDKTHCQHLAAKEEILL

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	10.81 RPM
SRP017611_kidney	0.00 RPM	11.20 RPM
SRP017611_liver	0.00 RPM	3.96 RPM
SRP040447_lung	0.00 RPM	12.61 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.84 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1225 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1225 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015607	1 retrocopy	retro_cfam_849,
Choloepus hoffmanni	ENSCHOG00000012658	1 retrocopy	retro_chof_602,
Cavia porcellus	ENSCPOG00000025598	1 retrocopy	retro_cpor_1225 ,
Dasypus novemcinctus	ENSDNOG00000018606	1 retrocopy	retro_dnov_1293,
Homo sapiens	ENSG00000152382	1 retrocopy	retro_hsap_3928,
Gorilla gorilla	ENSGGOG00000008168	1 retrocopy	retro_ggor_2644,
Mus musculus	ENSMUSG00000026563	1 retrocopy	retro_mmus_865,
Otolemur garnettii	ENSOGAG00000007621	1 retrocopy	retro_ogar_1989,
Pongo abelii	ENSPPYG00000000557	1 retrocopy	retro_pabe_3243,
Pan troglodytes	ENSPTRG00000001627	1 retrocopy	retro_ptro_2671,
Tupaia belangeri	ENSTBEG00000007283	1 retrocopy	retro_tbel_3501,