RetrogeneDB ID: retro_ptro_3107

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:41462567..41463323(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLIC4
• Ensembl ID: ENSPTRG00000000350
• Aliases: None
• Description: None

Sequence

>retro_ptro_3107
ATGGCGTTGTCGATGCCGTTGAACGGGCTGAAGGAGGAGGACAAAGAGCCCCTCATTGAGCTCCTCGTCAAAGCTGGCAG
TGATGGTGAAAGCATAGGAAACTGCCCCTTTTCCCAGAGGTTCTTCATGATTCGTTGACTCAAAGGAGTTGTATTTAGTG
TCACAACTGTTGACCTGAAATGGAAGCCTGCAGACCTTCAGAACTTAGCTCCCAGGACCCACCCACCGTTTGTAAGTTTC
AACAGTGAAGTCAAAACGGATGTAAGTAAGATTGAGGAATTTCTTGAAGAAGTCTTACGCCCTCCCAAGTACTTAAAGCT
TTCACCAAAACACCCAGAATCAAATACTGCTGGAATGGACATCTTTGCCAAATTCTCTGCATTTATCAAGAATTGAAGGC
GAGAGGCTAATGAAGCACTGGAGAAGGATCTCCTGAAAACCCTGCAGAAACTGGATAAATATCTGAATTCTCCTCTCCCT
GATGAAATTGATGAAAATAGTATAGAGGACATTAAGTTTTCTACACATAAATTTCTGGATGGCAATGAAATGACATTAGC
TGATTGCAGCCTGCTCCCCAAACTGCATATTGTCAAGGTGGTGGCCAAAAAATATCACAACTTTGATATTCCAAAAGAGA
TGACTGGCATCTGGAGATACCTAACTAATGCATATAGTAGGGACGAGTTCATCAATACCTGTCCCAGTGATAAGGAGGTT
GAAATAGCATATAGTGATGCCAAAAGACCCACCAAG

Alignment

ORF - retro_ptro_3107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALSMPLNGLKEEDKEPLIELFVKAGSDGESIGNCPFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLA
          MALSMPLNGLKEEDKEPLIEL.VKAGSDGESIGNCPFSQR.FMI..LKGVVFSVTTVDLK.KPADLQNLA
Retrocopy MALSMPLNGLKEEDKEPLIELLVKAGSDGESIGNCPFSQRFFMIR*LKGVVFSVTTVDLKWKPADLQNLA

Parental  PGTHPPFITFNSEVKTDVNKIEEFLEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSRPEANEAL
          P.THPPF..FNSEVKTDV.KIEEFLEEVL.PPKYLKLSPKHPESNTAGMDIFAKFSA.IKN.R.EANEAL
Retrocopy PRTHPPFVSFNSEVKTDVSKIEEFLEEVLRPPKYLKLSPKHPESNTAGMDIFAKFSAFIKN*RREANEAL

Parental  ERGLLKTLQKLDEYLNSPLPDEIDENSMEDIKFSTRKFLDGNEMTLADCNLLPKLHIVKVVAKKYRNFDI
          E..LLKTLQKLD.YLNSPLPDEIDENS.EDIKFST.KFLDGNEMTLADC.LLPKLHIVKVVAKKY.NFDI
Retrocopy EKDLLKTLQKLDKYLNSPLPDEIDENSIEDIKFSTHKFLDGNEMTLADCSLLPKLHIVKVVAKKYHNFDI

Parental  PKEMTGIWRYLTNAYSRDEFTNTCPSDKEVEIAYSDVAKRLTK
          PKEMTGIWRYLTNAYSRDEF.NTCPSDKEVEIAYSD.AKR.TK
Retrocopy PKEMTGIWRYLTNAYSRDEFINTCPSDKEVEIAYSD-AKRPTK

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	36.27 RPM
SRP007412_cerebellum	0.11 RPM	19.68 RPM
SRP007412_heart	0.03 RPM	182.69 RPM
SRP007412_kidney	0.05 RPM	200.61 RPM
SRP007412_liver	0.00 RPM	30.70 RPM
SRP007412_testis	0.00 RPM	52.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3107 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3107 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 38 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,
Pan troglodytes	ENSPTRG00000017982	2 retrocopies	retro_ptro_1238, retro_ptro_724,
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,