RetrogeneDB ID: retro_ptro_396

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:217386046..217386754(-)
• 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_396
GAGCCCCTCATCAAGCTCTTCATCAAGGCTGGCACTGATGGTGAAAGGACAGGAAACTGCCCCCTTTCCCAGAGGCTATT
CATGATTCTTTGGCTCAAAGGAGTTGTATTCAGTGTTACAATTGCTGACCTGAAAAGGAGGCCTGCAGACCTGCAAAACT
TGCCCCTCAGGACCCACCCACCATTTATAACTTTCAACAATGAGGTCAAAACAAATGTAAATAAGATTGAGGAATTTCTT
GAAGACATCGTATGCCCTCCCAAGTACTTAGAGCTTTCACCAAAACACGCAGAATCAAATACTGCTGGAATGGACGTCTT
TGCCAAATTCTCTGCATATATCAAGAATTCAAGGCCAGAGGCTAATGAAGCACTGGTGAAGAGTCTCTTGAAAACCCTGC
AGAAACTCAATGAATATCTGAATCCTCTCCTCCCTGATGAAATTGATAAAAATAGTAGGGAGGACATTACATTTTCTATA
TGTAAATTTCCGGTTGGCAATGAAATGACATTAGCTGACCTGCTGCCCAAACTGCATATTGTCAAGGTGGTGGCCAAAAG
ATATCACAACTTTGATATTCCAGAAAGAATGACTGGCATATGGAGCTATCTAACTAACGCATATAAAAGGGATGAGTTTA
CCAATACCTGTCCCCATGGTAAGAAGGTTGAAATAGCCTATAGTGACGTATCCAAAAAACTCAACAAG

Alignment

ORF - retro_ptro_396 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 94.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPLIELFVKAGSDGESIGNCPFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLAPGTHPPFITFNSEVK
          EPLI.LF.KAG.DGE..GNCP.SQRLFMILWLKGVVFSVT..DLKR.PADLQNL...THPPFITFN.EVK
Retrocopy EPLIKLFIKAGTDGERTGNCPLSQRLFMILWLKGVVFSVTIADLKRRPADLQNLPLRTHPPFITFNNEVK

Parental  TDVNKIEEFLEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSRPEANEALERGLLKTLQKLDEYL
          T.VNKIEEFLE...CPPKYL.LSPKH.ESNTAGMD.FAKFSAYIKNSRPEANEAL...LLKTLQKL.EYL
Retrocopy TNVNKIEEFLEDIVCPPKYLELSPKHAESNTAGMDVFAKFSAYIKNSRPEANEALVKSLLKTLQKLNEYL

Parental  NSPLPDEIDENSMEDIKFSTRKFLDGNEMTLADCNLLPKLHIVKVVAKKYRNFDIPKEMTGIWRYLTNAY
          N..LPDEID.NS.EDI.FS..KF..GNEMTLAD..LLPKLHIVKVVAK.Y.NFDIP..MTGIW.YLTNAY
Retrocopy NPLLPDEIDKNSREDITFSICKFPVGNEMTLAD--LLPKLHIVKVVAKRYHNFDIPERMTGIWSYLTNAY

Parental  SRDEFTNTCPSDKEVEIAYSDVAKRLTK
          .RDEFTNTCP..K.VEIAYSDV.K.L.K
Retrocopy KRDEFTNTCPHGKKVEIAYSDVSKKLNK

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	0.00 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_396 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_396 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_219
Callithrix jacchus	retro_cjac_1713

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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,