RetrogeneDB ID: retro_cpor_535

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_181:1258499..1258979(+)
• Located in intron of: ENSCPOG00000005918

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B10
• Ensembl ID: ENSCPOG00000009594
• Aliases: None
• Description: None

Sequence

>retro_cpor_535
AACTTAAAGAAGAAGCAGGCTCACAACTTGGAGGACTTCCAGCAAGTTCTCAAGGTGGATCTTTTAGGCACTTTCAATGT
AATCCACCTGGTGGCTGATAAAATGGGCCAGAATGAACCAGACCAGGGGAGCCAACATGGGGTTACCCTCAACACTGCCA
GTGTGGCTGACTTTGAGGGTCAAGTTGGACAAGCTGCATACTCTGCATCCAAAGGAAGCATAGTGGGCATGACACTGCCC
ATTGCTTGGGATCTGGCTACCATAGGCATCCAGGTCATGACCACTGCTCCAGGCTTATGTGGCACCCCATTGTTGACTAA
CCTACCGGAAAACGTAAGCAACTTCTTGGCCAGCCAGGTACCCTTCTCCACGCAACTCTGGGAACCCTGCTGAGTATGCT
CATCTGGTACAGACCATAATCGCACACTCATTCCTCCATTAAGAGGTTATCCGGCTAGATGGGGCCATGCCATGCAGCCT

Alignment

ORF - retro_cpor_535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.01 %
• Parental protein coverage: 61.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NLKKKQAHNLEDFQRVLNVNLLGTFNVIRLVAGEMGQNEPDEGGQRGIIINTASVAAFEGQVGQAAYSAS
          NLKKKQAHNLEDFQ.VL.V.LLGTFNVI.LVA..MGQNEPD.G.Q.G...NTASVA.FEGQVGQAAYSAS
Retrocopy NLKKKQAHNLEDFQQVLKVDLLGTFNVIHLVADKMGQNEPDQGSQHGVTLNTASVADFEGQVGQAAYSAS

Parental  KGGIVGMTLPIARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVRNFLASQVPFPTRL-GDPAEYAHLVQTI
          KG.IVGMTLPIA.DLA.IGI.VMT.APGL.GTPLLT.LPE.V.NFLASQVPF.T.L.G.PAEYAHLVQTI
Retrocopy KGSIVGMTLPIAWDLATIGIQVMTTAPGLCGTPLLTNLPENVSNFLASQVPFSTQL>GNPAEYAHLVQTI

Parental  IENPFLNGEVIRLDGAI-RMQP
          I...FL..EVIRLDGA...MQP
Retrocopy IAHSFLH*EVIRLDGAM<AMQP

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	30.31 RPM
SRP017611_kidney	0.00 RPM	112.22 RPM
SRP017611_liver	0.00 RPM	164.01 RPM
SRP040447_lung	0.05 RPM	41.36 RPM
SRP040447_skeletal_muscle	0.00 RPM	54.79 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_535 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_535 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,
Choloepus hoffmanni	ENSCHOG00000000939	1 retrocopy	retro_chof_582,
Cavia porcellus	ENSCPOG00000009594	1 retrocopy	retro_cpor_535 ,
Dipodomys ordii	ENSDORG00000004051	1 retrocopy	retro_dord_532,
Erinaceus europaeus	ENSEEUG00000005080	1 retrocopy	retro_eeur_379,
Felis catus	ENSFCAG00000013899	1 retrocopy	retro_fcat_1827,
Macropus eugenii	ENSMEUG00000008565	1 retrocopy	retro_meug_2184,
Myotis lucifugus	ENSMLUG00000000175	1 retrocopy	retro_mluc_4,
Otolemur garnettii	ENSOGAG00000002951	1 retrocopy	retro_ogar_1823,
Tarsius syrichta	ENSTSYG00000005340	3 retrocopies	retro_tsyr_1000, retro_tsyr_1542, retro_tsyr_2078,
Xenopus tropicalis	ENSXETG00000007721	1 retrocopy	retro_xtro_39,