RetrogeneDB ID: retro_cpor_1490

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:53974918..53975667(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLIC4
• Ensembl ID: ENSCPOG00000004010
• Aliases: None
• Description: None

Sequence

>retro_cpor_1490
TCGATACTGGTGAATGGGCTGATGGAGGAGTACAAAGAGCTCTTCATCGAACTCTTTTTCAAGGCTGGCAGGATGGGGAA
AACATAGGGAACTGTCCTTTCTCCTAGATGCTCTTCATGATTCTTTGCCTCAAAGGAGTTGTGCTTATTGTCTCAACCAT
GGACCTGAAAAGGAAGGCTACAAACCTCCAGAACTTGGCTTCTGGGATCCACCCACTGTTTATGACCTTCAACAACAAAG
TCAGAAAGGATGTCAGTAAGATTGAGGAATTTCTTGAAGAAGTGTTATGTGCTCCCAAGTACTTAAAGCCTTCACCAAAA
CACCCAGTGTCAAATACTGTTGGCATTGATATCTTTGCCAAATTCTCTGGTTATATCAAGAATGTGAGGCCAGAGGCCAA
TGAAACACTAGAGAGAGGTCTTTTGAAAATACTGCAGAAACTGGCTGAGTATTTGTATTCTCCCTTACCTGATGAAATTG
ATGAGAACAGTATGGAAGACATTAAATTTTCTAAGCATAAATTTCTGGATGGCAATGAAATAACATTAGCTGATTGCAAC
CTGGTTTCCAGACTGCACATTGTCAAGATGGTGACCGAGAAATATTGCAACGTCAATATTCCAAAAGGAATGACTGGCAT
CTGGAGATACTTAACTAATGCTTGTAGTAGGAAGGAGTTCACCAATATCTGTCCCAGTGATAAGGAGGTCAAAATACCCA
ACAGTGATGTCATAAAAAGACTTACCAGG

Alignment

ORF - retro_cpor_1490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.1 %
• Parental protein coverage: 98.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SMPLNGLKEEDKEPLIELFVKAG-SDGESIGNCPFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLAPG
          S...NGL.EE.KE..IELF.KAG..DGE.IGNCPFS..LFMIL.LKGVV..V.T.DLKRK...LQNLA.G
Retrocopy SILVNGLMEEYKELFIELFFKAG<QDGENIGNCPFS*MLFMILCLKGVVLIVSTMDLKRKATNLQNLASG

Parental  THPPFITFNNEVKTDVNKIEEFLEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSRPEANEALER
          .HP.F.TFNN.V..DV.KIEEFLEEVLC.PKYLK.SPKHP.SNT.G.DIFAKFS.YIKN.RPEANE.LER
Retrocopy IHPLFMTFNNKVRKDVSKIEEFLEEVLCAPKYLKPSPKHPVSNTVGIDIFAKFSGYIKNVRPEANETLER

Parental  GLLKTLQKLDEYLNSPLPDEIDENSMEDIKFSTRKFLDGNEMTLADCNLLPKLHIVKVVAKKYRNFDIPK
          GLLK.LQKL.EYL.SPLPDEIDENSMEDIKFS..KFLDGNE.TLADCNL...LHIVK.V..KY.N..IPK
Retrocopy GLLKILQKLAEYLYSPLPDEIDENSMEDIKFSKHKFLDGNEITLADCNLVSRLHIVKMVTEKYCNVNIPK

Parental  GMTGIWRYLTNAYSRDEFTNTCPSDKEVEIAYSDVAKRLTK
          GMTGIWRYLTNA.SR.EFTN.CPSDKEV.I..SDV.KRLT.
Retrocopy GMTGIWRYLTNACSRKEFTNICPSDKEVKIPNSDVIKRLTR

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	0.06 RPM	41.18 RPM
SRP017611_kidney	0.00 RPM	104.16 RPM
SRP017611_liver	0.00 RPM	34.91 RPM
SRP040447_lung	0.13 RPM	90.92 RPM
SRP040447_skeletal_muscle	0.10 RPM	20.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1490 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1490 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 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007591	10 retrocopies	retro_chof_1284, retro_chof_1401, retro_chof_1446, retro_chof_1654, retro_chof_2177, retro_chof_2673, retro_chof_784, retro_chof_789, retro_chof_808, retro_chof_947,
Callithrix jacchus	ENSCJAG00000020833	2 retrocopies	retro_cjac_1713, retro_cjac_461,
Cavia porcellus	ENSCPOG00000004010	1 retrocopy	retro_cpor_1490 ,
Homo sapiens	ENSG00000169504	2 retrocopies	retro_hsap_4143, retro_hsap_4678,
Gorilla gorilla	ENSGGOG00000005586	2 retrocopies	retro_ggor_1579, retro_ggor_2783,
Macropus eugenii	ENSMEUG00000008789	1 retrocopy	retro_meug_780,
Macaca mulatta	ENSMMUG00000002416	2 retrocopies	retro_mmul_1183, retro_mmul_2488,
Mus musculus	ENSMUSG00000037242	2 retrocopies	retro_mmus_2259, retro_mmus_945,
Nomascus leucogenys	ENSNLEG00000008997	3 retrocopies	retro_nleu_1457, retro_nleu_1785, retro_nleu_2168,
Otolemur garnettii	ENSOGAG00000014620	1 retrocopy	retro_ogar_2672,
Pongo abelii	ENSPPYG00000001715	3 retrocopies	retro_pabe_219, retro_pabe_3466, retro_pabe_3632,
Pan troglodytes	ENSPTRG00000000350	3 retrocopies	retro_ptro_2816, retro_ptro_3107, retro_ptro_396,
Pteropus vampyrus	ENSPVAG00000005838	1 retrocopy	retro_pvam_812,
Ictidomys tridecemlineatus	ENSSTOG00000002184	1 retrocopy	retro_itri_52,
Tarsius syrichta	ENSTSYG00000008978	1 retrocopy	retro_tsyr_252,
Vicugna pacos	ENSVPAG00000007699	1 retrocopy	retro_vpac_475,