RetrogeneDB ID: retro_cpor_471

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:30959401..30959657(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM2D1
• Ensembl ID: ENSCPOG00000012287
• Aliases: None
• Description: None

Sequence

>retro_cpor_471
AAAGATCCAACAAATGGTGCTACACAAGAACCAGGTAACTGTGCAAACCACACAGCTTGACTTTCATGTTGCCCAGCACA
CAATATAACATGTAAGGATTTCAGAGGCAATCAAACACATTTTACTGGAAATGCCGGTGGTTTTCTCAAACCATATCTTG
ACAAAATATAAATGGCTATGTAAACAAAGTGGCATTATCTCTTTTACTGGATGGCTGGGAGCAGACTGATTTTACTTTGG
GTACCCTTGGGTAGGC

Alignment

ORF - retro_cpor_471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.95 %
• Parental protein coverage: 58.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDPKINDATQEPVNCTNYTAHVPCLPAPNIICKDSSGNETHFTGKEVGFYK-VVPCRNVNGYSYKVAVAL
          KDP..N.ATQEP.NC.N.TA...C.PA.NI.CKD..GN.THFTG...GF.K......N.NGY..KVA..L
Retrocopy KDPT-NGATQEPGNCANHTA*LSCCPAHNITCKDFRGNQTHFTGNAGGFLK<TIS*QNINGYVNKVALSL

Parental  SLFLGWLGADRFYL-GYPALG
          .L..GW...D.F.L.GYP..G
Retrocopy -LLDGWEQTD-FTL<GYPWVG

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	10.70 RPM
SRP017611_kidney	0.00 RPM	19.58 RPM
SRP017611_liver	0.00 RPM	15.84 RPM
SRP040447_lung	0.00 RPM	11.88 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.86 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_471 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_471 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011705	1 retrocopy	retro_amel_1290,
Canis familiaris	ENSCAFG00000018838	1 retrocopy	retro_cfam_1213,
Choloepus hoffmanni	ENSCHOG00000013535	1 retrocopy	retro_chof_1494,
Cavia porcellus	ENSCPOG00000012287	1 retrocopy	retro_cpor_471 ,
Equus caballus	ENSECAG00000015035	1 retrocopy	retro_ecab_556,
Erinaceus europaeus	ENSEEUG00000001567	1 retrocopy	retro_eeur_708,
Loxodonta africana	ENSLAFG00000013979	1 retrocopy	retro_lafr_662,
Mus musculus	ENSMUSG00000028563	2 retrocopies	retro_mmus_1412, retro_mmus_1981,
Rattus norvegicus	ENSRNOG00000007527	1 retrocopy	retro_rnor_1104,
Tupaia belangeri	ENSTBEG00000002089	3 retrocopies	retro_tbel_1156, retro_tbel_1730, retro_tbel_201,