RetrogeneDB ID: retro_ptro_266

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:219488927..219490050(+)
• Located in intron of: ENSPTRG00000002157

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_266
ATGGTGAACCAGGTTATCAAGTGCAAGGCTGCAGTTGCCTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGT
GGCACCCCCAAAGGCTCGTGAAGTTTGAATCAAGATAATTGCCACTGCAGTTTGCCACACCAATGCCTATACCCTGAGCA
GAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGTGGGAAGTGTTGGTGAGGGAGTT
GCTAAGCTGAAGGCGGGTGATAACTGTCATCCCATTTTACATCCCACAGTGTAGAGAATGCAAATTTTGTCTAAATCCTA
AAACTAACCTTTGCCAGAATATAAGAGTCACTCAAGGGAAAGGATTAGTGCCAGATGGTACCAGCAGATTTACTTGCAAA
GGAAAGACAATTTTACATTACATGGGAACCAGCACATTTTCTGAATGCACAGTTGTGGCTGATATCTCTGTTGCTAAAAT
AGATTCTTTAGCACCTTTGGATAAAGTCTGCCTTCTAGGTTGTGGCATTTCAGCTGGTTATGGTGCTGCTGTGAACAGTG
TCGAGGTGGGGCCTGGCTCTGTTTGGGCCGTCTTTGGCCTGGGAGGAGTTGGATTGACAGTTATCGTGGGCGGTAAAGTG
GCTGGTGCATCCCGGATCATTGGTGTGGACATCCATCAAGATAAATTTCCAAGGGCTAAAGAGTTTGGAGCCACTGAATG
TATGAACCGTCAGGATTTTAGTAAACCCATCCAGGAAGTGCTCATTGAGCTGACTGATGGAGGAGTGGACTACTCCTTTG
AATGTATTAGGAATGTCAAGGTCGTGAGAGCAGCACTTGAGGCATGTCAGCAGGGCTGGGGCATCAGTGTGGTGGTTGGA
GTAGCTGCTTCAGGTCAAGAAGTTGCCACTCGTCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGCACTGCCTTTGG
AGGGTGAAAGAGTGTAGAAAGTGTCCCAAAGTTGGTATCTGAATATGTGTCTAAAAAGATAAAAGTTGATGAATTTGTGA
CTCACAATCTGTCTTTTGATGAAATTAACAAAGCCTTTGAACTGTTGCATTCTGGAAAGAGCATTCGAACTGTTGTCAAG
ATT

Alignment

ORF - retro_ptro_266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANEVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVILGHEGA
          M.N.VIKCKAAVAWEAGKPLSIEEIEVAPPKA.EV.IKIIATAVCHT.AYTLS.ADPEGCFPVILGHEGA
Retrocopy MVNQVIKCKAAVAWEAGKPLSIEEIEVAPPKAREV*IKIIATAVCHTNAYTLSRADPEGCFPVILGHEGA

Parental  GIVESVGEGVTKLKAGD-TVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILH
          GIV.SVGEGV.KLKAGD.TVIP.YIPQC.ECKFCLNPKTNLCQ.IRVTQGKGL.PDGTSRFTCKGKTILH
Retrocopy GIVGSVGEGVAKLKAGD>TVIPFYIPQCRECKFCLNPKTNLCQNIRVTQGKGLVPDGTSRFTCKGKTILH

Parental  YMGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIM
          YMGTSTFSE.TVVADISVAKID.LAPLDKVCLLGCGIS.GYGAAVN...V.PGSV.AVFGLGGVGL.VI.
Retrocopy YMGTSTFSECTVVADISVAKIDSLAPLDKVCLLGCGISAGYGAAVNSVEVGPGSVWAVFGLGGVGLTVIV

Parental  GCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAAL
          G.KVAGASRIIGVDI..DKF.RAKEFGATEC.N.QDFSKPIQEVLIE.TDGGVDYSFECI.NVKV.RAAL
Retrocopy GGKVAGASRIIGVDIHQDKFPRAKEFGATECMNRQDFSKPIQEVLIELTDGGVDYSFECIRNVKVVRAAL

Parental  EACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTHS
          EAC..GWG.SVVVGVAASG.E.ATRPFQLVTGRTWKGTAFGG.KSVESVPKLVSEY.SKKIKVDEFVTH.
Retrocopy EACQQGWGISVVVGVAASGQEVATRPFQLVTGRTWKGTAFGG*KSVESVPKLVSEYVSKKIKVDEFVTHN

Parental  LSFDEINKAFELMHSGKSIRTVVKI
          LSFDEINKAFEL.HSGKSIRTVVKI
Retrocopy LSFDEINKAFELLHSGKSIRTVVKI

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	0.09 RPM	26.79 RPM
SRP007412_cerebellum	0.07 RPM	30.29 RPM
SRP007412_heart	0.00 RPM	114.66 RPM
SRP007412_kidney	0.03 RPM	187.46 RPM
SRP007412_liver	0.03 RPM	169.86 RPM
SRP007412_testis	0.00 RPM	42.47 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_ptro_266 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AU298532	219489058	219489432	95.1	353	11	336
DC528916	219489058	219489432	95.1	353	11	336

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_266 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_330
Gorilla gorilla	retro_ggor_354
Pongo abelii	retro_pabe_359

---

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,