RetrogeneDB ID: retro_cpor_1520

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_92:5890679..5891273(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DERL1
• Ensembl ID: ENSCPOG00000011870
• Aliases: None
• Description: None

Sequence

>retro_cpor_1520
TTCCTCTATGGCTTCCAGATCTGGAGGCCCATCACTGCCACCTTTTATTTCCCTGTGAGTCCAGGAACTGAATTTCTTTA
TTTGCTCAATTTATATTTCTTATATCAGTATTCTACAAGACTTGAAGCAAGAATTTTAATGGGAGGCCAGCATACTATTT
ATTCATACTTCTCTTCACCTGGATTTGATTGTGATTATTGGCTTGACAGTGGATATACAGTTGATGATGATTACTCTGAT
CATGTAAGTGTTTTGTGTCTGGGCTCGGCTTAACAGAGACGTGATTGTGTGATTTTGGTTTGGAGCATGATTCAAGGTCT
GTTATTTACACTGGGTTACCCTTGGATTCAACTACATCGACAGAGGTTTGGTGATCAATGAGTTATTTGGAAATCTTATC
AGGCATCTTTATTTCTTCCTAATAAAGACACTCAATGGACTTGTGGGGGAAGAAATGTTTTACCTACATCTACATTTTTG
TACCACTGGCTGACCAGCAGGAGAGGTGGGGCATCCGAATTTGGGGTGGCTCCTGCTAGTATGACCAGAATGGCAGAGGT
GGATGACACAACTGGGCCAGGGCTTTCAACTTGG

Alignment

ORF - retro_cpor_1520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.35 %
• Parental protein coverage: 78.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FLYRFQIWRPITATFYFPVGPGTGFLYLVNLYFLYQYSTRLETGA-FDGRPADYLFMLLFNWI-CIVITG
          FLY.FQIWRPITATFYFPV.PGT.FLYL.NLYFLYQYSTRLE....F.GRPA.YLF.LLF.WI..IVI.G
Retrocopy FLYGFQIWRPITATFYFPVSPGTEFLYLLNLYFLYQYSTRLEARI<FNGRPAYYLFILLFTWI<LIVIIG

Parental  LAMDMQLLMIPLIMSVLYVWAQLNRDMMVSFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVGHLY
          L..D.QL.MI.LIM.V..VWA.LNRD..V.FWFG..FK.CYL.WV.LGFNYI..G.VINEL.GNL..HLY
Retrocopy LTVDIQLMMITLIM*VFCVWARLNRDVIV*FWFGA*FKVCYLHWVTLGFNYIDRGLVINELFGNLIRHLY

Parental  FFLMFRYPMDLGGRNF-LSTPQFLYRWLPSRRGGVSGFGVPPASVRRAA--DQNGGGGRHNW
          FFL........G...F.L.T..FLY.WL.SRRGG.S.FGV.PAS..R.A..D...G.G...W
Retrocopy FFLIKTLNGLVGEEMF<LPTSTFLYHWLTSRRGGASEFGVAPASMTRMAEVDDTTGPGLSTW

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	16.22 RPM
SRP017611_kidney	0.00 RPM	47.32 RPM
SRP017611_liver	0.00 RPM	43.57 RPM
SRP040447_lung	0.00 RPM	37.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	20.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1520 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1520 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006519	1 retrocopy	retro_amel_364,
Canis familiaris	ENSCAFG00000000974	1 retrocopy	retro_cfam_754,
Cavia porcellus	ENSCPOG00000011870	1 retrocopy	retro_cpor_1520 ,
Myotis lucifugus	ENSMLUG00000009085	1 retrocopy	retro_mluc_2035,
Mustela putorius furo	ENSMPUG00000001132	1 retrocopy	retro_mputfur_1082,
Mus musculus	ENSMUSG00000022365	1 retrocopy	retro_mmus_919,
Rattus norvegicus	ENSRNOG00000005551	2 retrocopies	retro_rnor_1206, retro_rnor_2717,
Sarcophilus harrisii	ENSSHAG00000011915	1 retrocopy	retro_shar_588,