RetrogeneDB ID: retro_ptro_3191

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:27686036..27687506(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMEK2
• Ensembl ID: ENSPTRG00000011933
• Aliases: None
• Description: None

Sequence

>retro_ptro_3191
ATGGCGGGCCTGAGGTACAGTGTAAAAGTCTATGTCCTGAACGAAGACGAGGAATGGAACAATCTAGGCACTGGTCAGAT
CTCATCCACCTATGACGAGCAGTTCCAGGGCATGTCGCTGCTTGTTCGGTCAGATTCAGATGGGTCAGTCATCCTGCGGT
CACAGATACCTCCAGACAGGCCCTATGGGAAATACCAAGAGACACTAATTGTTTGGTATGAAGCTGAGAACCAGGGTTTG
GTGCTAAAATTCCAGGACCCAGCTGGCTGCCAGGATATTTGGAAAGAAATTTGCCAAGCTCAAGGTAAGGATCCGTCTAT
CCAAACCGCAGTGAACATTTCAGATGAACCAGAGGAAGACTTTAATGAAATGTCAGTAATTAGTAATATGGTTGTGCTGC
CTGACTGTGAACTCAATACACTTGATCAAATTGCTGACATAGTTACCTCAGTTTTCTCGTCACCTATTACGGATAGGGAA
AGACTGGCTGAGATCTTGAAAAATGAGGCTTATATTCCAAAACTACTGCAACTGTTCCACACTTGTGAAAATCTACAGAA
TACTGAAGGTTTACACCATTTGTATGAAATTATTAAGGGAATTTTATTCCTCAACGAGGCATGTCTGTTTGAGATAATGT
TTTCTGACGAGTGTATCATGGATGTGGTGGGATGCCTTGAGTATGACCCTGCTTTGGATCAGCCAAAAAGGCATAGGGAC
TTCTTGACCAACGATGCAAAGTTCAAGGAAGTTATACCAATAACTAACTCTGAACTTAGGCAAAAAATACATCAGACATA
CAGATTACAGTACATTTATGACATTCTTTTGCCTGTGCCTTCCATATTTGAAGATAATTTTCTTTCTACACTTACAACTT
TTATTTTCTCCAACAAGGCTGAGATAGTAAGCATGCTGCAGAAAGATCACAAATTTTTGTATGAAGTTTTTGCACAGTTA
AAGGATGAGACTACACATGATGATAGACGGTGTGAATTGCTATTTTTTTTCAAGGAGTTATGTTCATTTTCTCAGGCATT
ACAGCCTCAAAGCAAGGATGCACTATTTGAAACGTTGATACAGTTGGGAGTTCTTCCTGCTCTTAAAATCGTAATGATCA
GGGATGATTTGCAAGTAAGGTCAGCTGCTGCAGTTATATGTGCTTATCTAGTGGAGTACAGTCCATCCAGGATCCGAGAA
TTTATAATTTCAGAAGCTCACGTGTGCAAAGATAGTGACCTTTTCATTAATGTAATAATTAAACAAATGATCTGTGATAC
TGAACCTGAGTTAGGAGGTGCTGTTCATTTGATGGTAGTTCTGCATACTCTACTTGATCCACGCAACATGCTGACAACAC
CTGAGAAAAGTGAAAGAAGTGAATTTCTACATTTCTTCTACAAACATTGCATGCATAAATTTACAGCACCACTTTTGGCT
GCCACCTCACAACACAACTGTGAGGAGGAT

Alignment

ORF - retro_ptro_3191 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.8 %
• Parental protein coverage: 57.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVDELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
          M...R..VKVY.LNED..W...GTG..SSTY.....GMSLLVR..SDGS..L.S.I.P...Y.K.Q.TLI
Retrocopy MAGLRYSVKVYVLNEDEEWNNLGTGQISSTYDEQFQGMSLLVRSDSDGSVILRSQIPPDRPYGKYQETLI

Parental  VWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELN
          VW.EAEN..L.L.FQ..AGC..IW..ICQ.QGKDPS........DE.EE..F.EM...S....LP.CELN
Retrocopy VWYEAENQGLVLKFQDPAGCQDIWKEICQAQGKDPSIQTAVNISDEPEED-FNEMSVISNMVVLPDCELN

Parental  KLEEIADLVTSVLSSPIR-REKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATL
          .L..IAD.VTSV.SSPI..RE.LA..L.NE.YI.KLLQLF..CENL.NTEGLHHLYEII.GILFLN.A.L
Retrocopy TLDQIADIVTSVFSSPITDRERLAEILKNEAYIPKLLQLFHTCENLQNTEGLHHLYEIIKGILFLNEACL

Parental  FEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPT
          FE.MFSDECIMDVVGCLEYDPAL.QPKRHR.FLT..AKFKEVIPIT.SELRQKIHQTYR.QYI.DI.LP.
Retrocopy FEIMFSDECIMDVVGCLEYDPALDQPKRHRDFLTNDAKFKEVIPITNSELRQKIHQTYRLQYIYDILLPV

Parental  PSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQP
          PS.FE.NFLSTLT.FIF.NK.EIVSMLQ.D.KFL.EVFAQL.DE.T.DD.R.EL....KE.C.FSQ.LQP
Retrocopy PSIFEDNFLSTLTTFIFSNKAEIVSMLQKDHKFLYEVFAQLKDETTHDDRRCELLXXXKELCSFSQALQP

Parental  QNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVV
          Q..DA.F.TL..LG.LPAL.IVM..DDLQVRSAA..I..YLVE.SPS..REF...EA....D..L.INV.
Retrocopy QSKDALFETLIQLGVLPALKIVMIRDDLQVRSAAAVICAYLVEYSPSRIREFIISEAHVCKDSDLFINVI

Parental  IEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDKCEK
          I.QMICDT.PELGGAV.LM..L.TL.DP.NML.T..K.E.SEFL.FFY.HCMH..TAPLL..TS...CE.
Retrocopy IKQMICDTEPELGGAVHLMVVLHTLLDPRNMLTTPEKSERSEFLHFFYKHCMHKFTAPLLAATSQHNCEE

Parental  D
          D
Retrocopy D

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	24.90 RPM
SRP007412_cerebellum	0.00 RPM	46.64 RPM
SRP007412_heart	0.00 RPM	26.58 RPM
SRP007412_kidney	0.00 RPM	65.48 RPM
SRP007412_liver	0.00 RPM	42.39 RPM
SRP007412_testis	1.37 RPM	80.62 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3191 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3191 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3191 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4799
Macaca mulatta	retro_mmul_238
Oryctolagus cuniculus	retro_ocun_9
Bos taurus	retro_btau_232
Sus scrofa	retro_sscr_1187
Canis familiaris	retro_cfam_226
Equus caballus	retro_ecab_23

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003843	1 retrocopy	retro_amel_48,
Bos taurus	ENSBTAG00000000545	1 retrocopy	retro_btau_232,
Canis familiaris	ENSCAFG00000002860	1 retrocopy	retro_cfam_226,
Equus caballus	ENSECAG00000013819	1 retrocopy	retro_ecab_23,
Echinops telfairi	ENSETEG00000002420	1 retrocopy	retro_etel_1699,
Felis catus	ENSFCAG00000026457	1 retrocopy	retro_fcat_13,
Homo sapiens	ENSG00000138041	1 retrocopy	retro_hsap_4799,
Loxodonta africana	ENSLAFG00000017825	1 retrocopy	retro_lafr_791,
Myotis lucifugus	ENSMLUG00000003875	1 retrocopy	retro_mluc_994,
Macaca mulatta	ENSMMUG00000007001	1 retrocopy	retro_mmul_238,
Mustela putorius furo	ENSMPUG00000002435	1 retrocopy	retro_mputfur_92,
Nomascus leucogenys	ENSNLEG00000009338	1 retrocopy	retro_nleu_1112,
Oryctolagus cuniculus	ENSOCUG00000006880	1 retrocopy	retro_ocun_9,
Otolemur garnettii	ENSOGAG00000009837	1 retrocopy	retro_ogar_140,
Pan troglodytes	ENSPTRG00000006638	1 retrocopy	retro_ptro_124,
Pan troglodytes	ENSPTRG00000011933	1 retrocopy	retro_ptro_3191 ,
Sus scrofa	ENSSSCG00000008398	1 retrocopy	retro_sscr_1187,
Ictidomys tridecemlineatus	ENSSTOG00000006276	1 retrocopy	retro_itri_63,
Tursiops truncatus	ENSTTRG00000000027	1 retrocopy	retro_ttru_1397,