RetrogeneDB ID: retro_pabe_219

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:11437150..11437796(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLIC4
• Ensembl ID: ENSPPYG00000001715
• Aliases: None
• Description: chloride intracellular channel protein 4 [Source:RefSeq peptide;Acc:NP_001124560]

Sequence

>retro_pabe_219
CCTTTCCCAGAGGCTCTTCATGATTCTTTGGCTCAAAGGAGTGTTTCATTCAGTGTTACAATTGTTGACCTGAAAAGGAG
GCCTGCAGACCTGCAAAACTTGCCCCTCAGAACCCACCCACCATTTATAACTTTCAACAATGAGGTCAAAACAGATGTAA
ATAAGATTGAGGAATTTCTTGAAGACATCTTATGCCCTCCCAAGTACTTAGAGCTTTCACCAAAACATGTGGAATCAAAC
TGCTGGAATGGACGTCTTTGCCAAATTCTCTGCATATATCAAGAATTCAAGGCCAGAGGCTAATGAAGCACTGGTGAAGA
GTCTCTTGAAAACCCTGCAGAAACTGAATGAATATCTGAATCCTCTCCTCCCTGATGAAACTGATAAAAATAGTAGGGAG
GATATTACATTTTCTACACGTAAATTTCTGGTTGGCAATGAAATGACATTAGCTGACCTGCTGCCCAAACTGCATATTGT
CAAGGTGGTGGCCAAAAAATATCACAACTTTGATATTCCAAAAAGAATGACTGGCCTATGGAGCTATCTAACTAATGCAT
ATAAAAGGGATGAGTTTACCAATACCTGTCCCCATGGTAAGAAGGTTGAAATAGCCTATAGTGATGTATCCAAAAAACTC
AACAAG

Alignment

ORF - retro_pabe_219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 86.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLAPGTHPPFITFNSEVKTDVNKIEEFLEEV-LCPPKY
          PF...L...L....V.FSVT.VDLKR.PADLQNL...THPPFITFN.EVKTDVNKIEEFLE...L.P...
Retrocopy PFPEALHDSLAQRSVSFSVTIVDLKRRPADLQNLPLRTHPPFITFNNEVKTDVNKIEEFLEDI<LMPSQV

Parental  LKLSPK-HPESNTAGMDIFAKFSAYIKNSRPEANEALERGLLKTLQKLDEYLNSPLPDEIDENSMEDIKF
          L....K......TAGMD.FAKFSAYIKNSRPEANEAL...LLKTLQKL.EYLN..LPDE.D.NS.EDI.F
Retrocopy LRAFTK<NMWNQTAGMDVFAKFSAYIKNSRPEANEALVKSLLKTLQKLNEYLNPLLPDETDKNSREDITF

Parental  STRKFLDGDEMTLADCNLLPKLHIVKVVAKKYRNFDIPKEMTGIWRYLTNAYSRDEFTNTCPSDKEVEIA
          STRKFL.G.EMTLAD..LLPKLHIVKVVAKKY.NFDIPK.MTG.W.YLTNAY.RDEFTNTCP..K.VEIA
Retrocopy STRKFLVGNEMTLAD--LLPKLHIVKVVAKKYHNFDIPKRMTGLWSYLTNAYKRDEFTNTCPHGKKVEIA

Parental  YSDVAKRLTK
          YSDV.K.L.K
Retrocopy YSDVSKKLNK

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	15.70 RPM
SRP007412_cerebellum	0.00 RPM	16.17 RPM
SRP007412_heart	0.00 RPM	59.97 RPM
SRP007412_kidney	0.00 RPM	161.33 RPM
SRP007412_liver	0.00 RPM	34.27 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_219 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_219 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_396
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,
Pongo abelii	ENSPPYG00000016456	2 retrocopies	retro_pabe_1514, retro_pabe_886,
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,