RetrogeneDB ID: retro_cpor_254

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_11:7716204..7716757(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED5
• Ensembl ID: ENSCPOG00000012192
• Aliases: None
• Description: None

Sequence

>retro_cpor_254
TTCACGACTTCCTTAGACAGCGACTTTATCTTTACCCTTCAGGCTGGCCAGAAGGAGTGATTTTACCAGTCCATGCCACT
GAAGGCCTCGCTGGAGATGAGTACCAAGTCTTAGAGGCAGCAGGATTAGATATTGATTTCCACATTGCCTGTCCCAAAGG
CAAAACCTTAGTTTTTGAACAAAGAAAATCAGATGGCGTCCACACTGTAGAAACTGAAGATGCTGGTTACATGTTCTGCT
TTGACAATACCTTAGCACCATTTCTGAGAAAGTAATTTTCTTTGAATTAATCTTCGATAATATGGAAGAACAGGCACAAG
AACAAGAAGACTGGAAGAAATGTATTACAGGTACAGATGAATTGGAGATGAAACTAGAAGACATCCTGGAATCCATCAAC
TGCATCAAGTCCAGAGTAAGCAAAAGTGGTCATATACAAACTCTTCTTAGAGCATTTGAAGTCCGTGATCCAAACATACA
AGAAAGTAACTTTGATAGAATCAATGTCTGGTCTGTGATTAATTTAGTTGTCATGGTGGTGGTGTCTGTGATA

Alignment

ORF - retro_cpor_254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 80.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FTPSLDSDFTFTLPAGQKECFYQPMPQKASLEI-EYQVLDGAGLDIDFHLASPNGKTLVFEQRKSDGVHT
          FT.SLDSDF.FTL.AGQKE.FYQ.MP.KASLE..EYQVL..AGLDIDFH.A.P.GKTLVFEQRKSDGVHT
Retrocopy FTTSLDSDFIFTLQAGQKE*FYQSMPLKASLEM<EYQVLEAAGLDIDFHIACPKGKTLVFEQRKSDGVHT

Parental  VETEVGDYMFCFDNTF-STISEKVIFFELILDNMGEHAQEQEDWKKYITGTDVLEMKLEDILESINSIKS
          VETE...YMFCFDNT..STISEKVIFFELI.DNM.E.AQEQEDWKK.ITGTD.LEMKLEDILESIN.IKS
Retrocopy VETEDAGYMFCFDNTL<STISEKVIFFELIFDNMEEQAQEQEDWKKCITGTDELEMKLEDILESINCIKS

Parental  RVSKSGHIQTLLKAFEARDRNIQESNFDRVNFWSMVNLVVMVVVSAI
          RVSKSGHIQTLL.AFE.RD.NIQESNFDR.N.WS..NLVVMVVVS.I
Retrocopy RVSKSGHIQTLLRAFEVRDPNIQESNFDRINVWSVINLVVMVVVSVI

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	7.30 RPM
SRP017611_kidney	0.10 RPM	21.88 RPM
SRP017611_liver	0.00 RPM	40.44 RPM
SRP040447_lung	0.00 RPM	21.46 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_254 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_254 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012192	1 retrocopy	retro_cpor_254 ,
Oryctolagus cuniculus	ENSOCUG00000012427	1 retrocopy	retro_ocun_566,
Rattus norvegicus	ENSRNOG00000000073	1 retrocopy	retro_rnor_620,
Ictidomys tridecemlineatus	ENSSTOG00000028196	1 retrocopy	retro_itri_155,