RetrogeneDB ID: retro_ptro_166

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:80206959..80208086(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADH5
• Ensembl ID: ENSPTRG00000016303
• Aliases: None
• Description: None

Sequence

>retro_ptro_166
ATGGCAAACCAGGTTATCAAGTACAAGGCTGCAGTTGCCTGGGAGGCTGGAAAGCCTCTCTCCACAGAGTAGGTAGAGGT
GGCACCCCCAAAGGCTCATGAAGTTCAAATTGAGATTGTTGCCACTGTGGTTTGCCACACTGACGCCTATACCCTGAGCA
GAGCTGGTCCTGAGGGTTGTTGTCCGGTGATCTTGGGACATGAAGGTGCTGGAATTGTGAAAAGTGTTGGTGAGGGAGTT
ACTAAGCTGAAGGCGGGTGACACTGTCATCTCACTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTAA
AACTAACCTTTGCCAGAAGATAAAGTCACACAAGGGAAAGGATTAATGCCAGATGGTACCAGCAGATTTACTTGCAAAGG
AAAGATAATTTTACATTACATGGGAATCAGCTCATTTTCTGAATACACAGTTGTGGCTGATATCTCTGTTGCCAAAATAG
ATCCTTTAGCACCTTTGGATAAAGTTGGCCTTCTAGGTTGTGGAATTTCAACTGGTTATGATCCTGCTGTGAACACTGCC
AAGCTGGAGCCTGACTCTGTTTGTGCCGTCTTTGGCCTGGGAGGAGTTGGATCGGGGGTTACCATGGGCTGTAAAGTGAC
TGGTGCATCCCAGATCATTGGTGTGGACATCAATAAAGATAAATTTGCAAGGGCCAAAGAACTTGGAGCCGCTGAATGCA
TTAGTTCTCAGGATTTTAGTAAACCCACCCAGGAAGTGCTCATTGAGATAATGAGCACTGATGGAGGAGTGGACTATTCC
TTTGAATGTACGGGTAATGTGAAGGTCATGAGAGCAGCACTTGAGGCATGTCACCAGGGCTAGGGCACCAATGTGGTGGT
TGGAGTAGCTGCTTCAGGTGAAGAAATTGCTGCTCATCCATTCCAGCTGGCAACAGGTCGCACATGGAAAGGCATTGCCT
TTGGAGGATGGAAGAGTATAGAAAGTGTCCCAAAGTTGGTGTCTGAATATATGTCCAAAAAGATAAAAGCTGATGAGTTT
ATGACTCACAATCTGTCTTTTGATGAAATTAACAAAGCCTTTGAACTCATGCATTCTGGAAAGAGCATTCGAACTGTTGT
CAAGATT

Alignment

ORF - retro_ptro_166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANEVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVILGHEGA
          MAN.VIK.KAAVAWEAGKPLS.E..EVAPPKAHEV.I.I.AT.VCHTDAYTLS.A.PEGC.PVILGHEGA
Retrocopy MANQVIKYKAAVAWEAGKPLSTE*VEVAPPKAHEVQIEIVATVVCHTDAYTLSRAGPEGCCPVILGHEGA

Parental  GIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIR-VTQGKGLMPDGTSRFTCKGKTILH
          GIV.SVGEGVTKLKAGDTVI.LYIPQCGECKFCLNPKTNLCQKI..VTQGKGLMPDGTSRFTCKGK.ILH
Retrocopy GIVKSVGEGVTKLKAGDTVISLYIPQCGECKFCLNPKTNLCQKIK<VTQGKGLMPDGTSRFTCKGKIILH

Parental  YMGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIM
          YMG.S.FSEYTVVADISVAKIDPLAPLDKV.LLGCGISTGY..AVNTAK.EP.SVCAVFGLGGVG..V.M
Retrocopy YMGISSFSEYTVVADISVAKIDPLAPLDKVGLLGCGISTGYDPAVNTAKLEPDSVCAVFGLGGVGSGVTM

Parental  GCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEM--TDGGVDYSFECIGNVKVMRA
          GCKV.GAS.IIGVDINKDKFARAKE.GA.ECI..QDFSKP.QEVLIE...TDGGVDYSFEC.GNVKVMRA
Retrocopy GCKVTGASQIIGVDINKDKFARAKELGAAECISSQDFSKPTQEVLIEIMSTDGGVDYSFECTGNVKVMRA

Parental  ALEACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVT
          ALEACH.G.G..VVVGVAASGEEIA..PFQL.TGRTWKG.AFGGWKS.ESVPKLVSEYMSKKIK.DEF.T
Retrocopy ALEACHQG*GTNVVVGVAASGEEIAAHPFQLATGRTWKGIAFGGWKSIESVPKLVSEYMSKKIKADEFMT

Parental  HSLSFDEINKAFELMHSGKSIRTVVKI
          H.LSFDEINKAFELMHSGKSIRTVVKI
Retrocopy HNLSFDEINKAFELMHSGKSIRTVVKI

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	0.05 RPM	26.79 RPM
SRP007412_cerebellum	0.00 RPM	30.29 RPM
SRP007412_heart	0.03 RPM	114.66 RPM
SRP007412_kidney	0.00 RPM	187.46 RPM
SRP007412_liver	0.03 RPM	169.86 RPM
SRP007412_testis	0.32 RPM	42.47 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_166 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_166 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_175
Pongo abelii	retro_pabe_453
Callithrix jacchus	retro_cjac_2933

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013007	1 retrocopy	retro_cfam_14,
Callithrix jacchus	ENSCJAG00000007198	2 retrocopies	retro_cjac_1029, retro_cjac_2933,
Homo sapiens	ENSG00000197894	3 retrocopies	retro_hsap_175, retro_hsap_330, retro_hsap_3607,
Gorilla gorilla	ENSGGOG00000028244	2 retrocopies	retro_ggor_2434, retro_ggor_354,
Myotis lucifugus	ENSMLUG00000002722	1 retrocopy	retro_mluc_1702,
Macaca mulatta	ENSMMUG00000003552	1 retrocopy	retro_mmul_299,
Mustela putorius furo	ENSMPUG00000009642	1 retrocopy	retro_mputfur_1625,
Nomascus leucogenys	ENSNLEG00000013946	3 retrocopies	retro_nleu_1772, retro_nleu_2636, retro_nleu_983,
Pongo abelii	ENSPPYG00000014946	3 retrocopies	retro_pabe_176, retro_pabe_359, retro_pabe_453,
Pan troglodytes	ENSPTRG00000016303	3 retrocopies	retro_ptro_166 , retro_ptro_2438, retro_ptro_266,
Sus scrofa	ENSSSCG00000009185	1 retrocopy	retro_sscr_659,
Xenopus tropicalis	ENSXETG00000009304	1 retrocopy	retro_xtro_57,