RetrogeneDB ID: retro_cpor_749

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:24536105..24536472(+)
• Located in intron of: ENSCPOG00000005675

Retrocopy information

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

Parental gene information

• Parental gene symbol: HN1L
• Ensembl ID: ENSCPOG00000005352
• Aliases: None
• Description: None

Sequence

>retro_cpor_749
GTTCTTTCAAACAGGCCTAAAGATTGGCCTCTAATATTTTCAAGAATAGCTAAAGAACCTCAGAACATACCCCAGAGGAC
AAGCCCCTCAGTGGAAAAAGGAAGTGATACCTTTAATGAATTGGCTCCTGTGAAGACCCACCTGAACCCAGCTGGTGTGA
AGAATAGTGACATTTTTGATTCCTCAGTTACTGCCACTTAACCATTAGTACACCCAAACAAACCCAAGGCCTGCACATTC
TCATGTGAAGAAAAACACTGAAAATTGGACCTTAACGCTGAAACAAGTACCTCACCCCCAAAAAGAGCTTCTCACACAGG
GCAGATTGAGAGAAATGGATCCCTAAAGTAGCCACAGTCCATGACCA

Alignment

ORF - retro_cpor_749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.12 %
• Parental protein coverage: 65.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VPSNRPN-RMASNIFGPT-EEPQNIPKRTNPPGGKGSGIFDESTPVQTRQRLNPPGGKASDIFGSPVTAA
          V.SNRP..R.ASNIF.....EPQNIP.RT.P...KGS..F.E..PV.T...LNP.G.K.SDIF.S.VTA.
Retrocopy VLSNRPK<RLASNIFKNS>KEPQNIPQRTSPSVEKGSDTFNELAPVKTH--LNPAGVKNSDIFDSSVTAT

Parental  SPLAHPNKPKDHILLCEGEDPKSDLKAATSTS-PQDELGTKGSSREVDHTKELEPMP
          .PL.HPNKPK.....CE....K.DL.A.TSTS.PQ.EL.T.G..RE.D......P.P
Retrocopy *PLVHPNKPKACTFSCEEKH*KLDLNAETSTS>PQKELLTQGRLREMDP*SSHSP*P

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	10.87 RPM
SRP017611_kidney	0.10 RPM	19.05 RPM
SRP017611_liver	0.00 RPM	7.05 RPM
SRP040447_lung	0.00 RPM	26.13 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.06 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_749 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_749 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008232	1 retrocopy	retro_amel_1019,
Cavia porcellus	ENSCPOG00000005352	2 retrocopies	retro_cpor_749 , retro_cpor_892,
Dipodomys ordii	ENSDORG00000007521	1 retrocopy	retro_dord_269,
Macropus eugenii	ENSMEUG00000008873	4 retrocopies	retro_meug_1471, retro_meug_1628, retro_meug_189, retro_meug_258,
Mus musculus	ENSMUSG00000024165	3 retrocopies	retro_mmus_1204, retro_mmus_655, retro_mmus_709,
Oryctolagus cuniculus	ENSOCUG00000015551	1 retrocopy	retro_ocun_275,
Pteropus vampyrus	ENSPVAG00000016673	1 retrocopy	retro_pvam_99,
Rattus norvegicus	ENSRNOG00000024661	2 retrocopies	retro_rnor_25, retro_rnor_560,
Sorex araneus	ENSSARG00000012440	1 retrocopy	retro_sara_335,
Sarcophilus harrisii	ENSSHAG00000012700	1 retrocopy	retro_shar_184,
Tursiops truncatus	ENSTTRG00000011377	1 retrocopy	retro_ttru_429,