RetrogeneDB ID: retro_ptro_1862

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:14792235..14794173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHBDF1
• Ensembl ID: ENSPTRG00000007527
• Aliases: None
• Description: None

Sequence

>retro_ptro_1862
CGAGAGTTGGTGGCCAAGATGAGCTTCCATGCAGCCGCAGCACTGATGAAAGGCTGCTCGATTAGGGATGGCACCTTGCG
CCGGGCACAGCGTCGAAGCTTCACTCCAGCCAGCTTTCTGGCGGAAAACACGAATTTCCCTGATGAGCTGGACACATCCT
TCTTTGCCCAGGAAGGTATCCTCCATGAAGAGCTGTCCACATACCCGGACAAAGTTTTTGAGTCCCCATCAGAGGCAGCA
CTCAAGGACTGGGAGAAGGCACCGGAGCAGGAGTACCTCACTGGCAGGGCCCTGGACCGCAGTGAGCTTGAGCCCAGCCA
CCTGATGCTGCCTTTGGAGCGAGGCTGGCGGAAGCAGGAAGACACCGCAGCCTCGCAGCCCAAGGGGCGGCTCCGACAGG
AGATGGTGAGCACCGCGGGGCCGCGGCGGAACCAGCGCATCGCTGTGCGGGTGCGCAAACTCTTCGCCCGGGAGAAGCGG
CTGCATGGGCTGAGCATGGTGGGACGGCTCAACAACCACACCTACCACAAGCACATCGACAGCTTCGTCAAGCGACAGAT
CGAGGACATGGACAGCCACAGGCCCTTCTTCACCCACTGGCTCACCTTCGTGCACTTGCTCGTCACCATTCTAGCCGTGT
GCATCTATGGCATCGTGCCCGTGGGCTTCTCACAGCATGAAACGGTGGACTCGATGCTGTGGAACCACTGGGTCTACGAG
AACGTCAAGTACGTGCAGCAGGAGAACTTCTGGATCGGGCCCAGCTCGGAGGCCCTCATCCACCTGGGTGCCAAGTTTTC
GCCTTGCATATGCCAGGATCCGCAGGTGCACAGCTTCATTCGCGCAGGGCGCGAGCACGAGAAGCACTCGGCCTGCTGCA
TGCACAACGACAGGTCGGGCTGCCTGCAGACCTCGGAGGAGGAGTGCTCGCCCATGCTGGCAATGTGGGTGAAGTGACCC
ATCCATTCCAGCGCCCCAGAGCTTGCCGGCCACAAGAGACAGTTTGGCTCTGTCTGTCACCAGGATCCCAGGGTATATGA
TGAGCCCTCCTGGGAAGACCCCCGTGAGTGGCCAGAAGACATTACCAAGTGGCCGATCTGCACCAGAAACAACCCTGGGA
ACCACACCAACCTTCCCCACATGGACTGTGTCATCACAGGACGGCCCTGCTGCATTGGCACCAACGGCGAGTGTGAGATC
ACCTCCCGGGAGTACTGTGACTTCATGAGGGGCTATTTCCATGAGGAGGCCACGCTCTGCTCTCAGGTGCACTGCATGGA
TGATGTGTGTGGGCTCCTGCCTTTCCTCAACCCTGAGGTGCCTGACCAGTTCTACCGCCTGTGGCTGTCCCTCTTCCTGC
ACACCAGGATCCTGCACTACCTGGTGTCCATCTGCTTCCAGATGACCGTCCCGCGGGACCTGGAGAAGCTGGCAGGGTGG
CACCACATAGCCATCATCTACCTGCTGAGTGGTGTCACTGGCAACCTGGCCAGTGCCATCTTCCTGCTGTACCGAGCAGA
GGTGGTTCCAGCTGGCTCCCAGTTTGGCATCCTGGCCTGCCTCTTCATGGAGCTCTTCCAGAGCTGGCAGATCCTGGAGC
GGCCCTGGCATGCCTTCTTCAAGCTGCTGGCTGTGGTGCTCTTCCTCTGCACCTTTGGGCTGCTGCCCTGGATCGACAAC
TTTGCCCACATTTCGGGGTTCATCAGTGGCCTCTTTCTCTCCTTCGCCTTCTAGCGCTACATCAGCTTCAGCAAGTTCCA
TCTGTACTGGAAATGCTGCCTGATCATCATCTTTCAGGTGGTCTTCCTGGGCCTCCTGGCTGGCCTGGTGGTCCTCTTCT
ACTTCTATCCTGTCTGCCGTGAGTGGTGTGAGTTCCTCACCTGCATCCCCTTCACTGATAATTTCTGCGAGAAGTACGAA
CTGGATGCTCAGCTCCAC

Alignment

ORF - retro_ptro_1862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.35 %
• Parental protein coverage: 75.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RESVAKMSFRAAAALMKGRSVRDGTFRRAQRRSFTPASFLEEDTTDFPDELDTSFFAREGILHEELSTYP
          RE.VAKMSF.AAAALMKG.S.RDGT.RRAQRRSFTPASFL.E.T..FPDELDTSFFA.EGILHEELSTYP
Retrocopy RELVAKMSFHAAAALMKGCSIRDGTLRRAQRRSFTPASFLAENT-NFPDELDTSFFAQEGILHEELSTYP

Parental  DEVFESPSEAALKDWEKAPEQADLTGGALDRSELERSHLMLPLERGWRKQKEGAAAPQPKVRLRQEVVST
          D.VFESPSEAALKDWEKAPEQ..LTG.ALDRSELE.SHLMLPLERGWRKQ.E..AA.QPK.RLRQE.VST
Retrocopy DKVFESPSEAALKDWEKAPEQEYLTGRALDRSELEPSHLMLPLERGWRKQ-EDTAASQPKGRLRQEMVST

Parental  AGPRRGQRIAVPVRKLFAREKRPYGLGMVGRLTNRTYRKRIDSFVKRQIEDMDDHRPFFTYWLTFVHSLV
          AGPRR.QRIAV.VRKLFAREKR..GL.MVGRL.N.TY.K.IDSFVKRQIEDMD.HRPFFT.WLTFVH.LV
Retrocopy AGPRRNQRIAVRVRKLFAREKRLHGLSMVGRLNNHTYHKHIDSFVKRQIEDMDSHRPFFTHWLTFVHLLV

Parental  TILAVCIYGIAPVGFSQHETVDSVLRNRGVYENVKYVQQENFWIGPSSEALIHLGAKFSPCMRQDPQVHS
          TILAVCIYGI.PVGFSQHETVDS.L.N..VYENVKYVQQENFWIGPSSEALIHLGAKFSPC..QDPQVHS
Retrocopy TILAVCIYGIVPVGFSQHETVDSMLWNHWVYENVKYVQQENFWIGPSSEALIHLGAKFSPCICQDPQVHS

Parental  FIRSAREREKHSACCVRNDRSGCVQTSEEECSSTLAVWVKWPIHPSAPELAGHKRQFGSVCHQDPRVCDE
          FIR..RE.EKHSACC..NDRSGC.QTSEEECS..LA.WVK.PIH.SAPELAGHKRQFGSVCHQDPRV.DE
Retrocopy FIRAGREHEKHSACCMHNDRSGCLQTSEEECSPMLAMWVK*PIHSSAPELAGHKRQFGSVCHQDPRVYDE

Parental  PSSEDPHEWPEDITKWPICTKNSAGNHTNHPHMDCVITGRPCCIGTKGRCEITSREYCDFMRGYFHEEAT
          PS.EDP.EWPEDITKWPICT.N..GNHTN.PHMDCVITGRPCCIGT.G.CEITSREYCDFMRGYFHEEAT
Retrocopy PSWEDPREWPEDITKWPICTRNNPGNHTNLPHMDCVITGRPCCIGTNGECEITSREYCDFMRGYFHEEAT

Parental  LCSQVHCMDDVCGLLPFLNPEVPDQFYRLWLSLFLHAGILHCLVSICFQMTVLRDLEKLAGWHRIAIIYL
          LCSQVHCMDDVCGLLPFLNPEVPDQFYRLWLSLFLH..ILH.LVSICFQMTV.RDLEKLAGWH.IAIIYL
Retrocopy LCSQVHCMDDVCGLLPFLNPEVPDQFYRLWLSLFLHTRILHYLVSICFQMTVPRDLEKLAGWHHIAIIYL

Parental  LSGVTGNLASAIFLPYRAEVGPAGSQFGILACLFVELFQSWQILARPWRAFFKLLAVVLFLFTFGLLPWI
          LSGVTGNLASAIFL.YRAEV.PAGSQFGILACLF.ELFQSWQIL.RPW.AFFKLLAVVLFL.TFGLLPWI
Retrocopy LSGVTGNLASAIFLLYRAEVVPAGSQFGILACLFMELFQSWQILERPWHAFFKLLAVVLFLCTFGLLPWI

Parental  DNFAHISGFISGLFLSFAFLPYISFGKFDLYRKRCQIIIFQVVFLGLLAGLVVLFYVYPVRCEWCEFLTC
          DNFAHISGFISGLFLSFAF..YISF.KF.LY.K.C.IIIFQVVFLGLLAGLVVLFY.YPV..EWCEFLTC
Retrocopy DNFAHISGFISGLFLSFAF*RYISFSKFHLYWKCCLIIIFQVVFLGLLAGLVVLFYFYPVCREWCEFLTC

Parental  IPFTDKFCEKYELDAQLH
          IPFTD.FCEKYELDAQLH
Retrocopy IPFTDNFCEKYELDAQLH

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	0.02 RPM	12.87 RPM
SRP007412_cerebellum	0.07 RPM	7.03 RPM
SRP007412_heart	0.00 RPM	8.57 RPM
SRP007412_kidney	0.00 RPM	26.31 RPM
SRP007412_liver	0.00 RPM	10.77 RPM
SRP007412_testis	0.42 RPM	1.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1862 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1862 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2754
Gorilla gorilla	retro_ggor_1916

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000007384	1 retrocopy	retro_hsap_2754,
Gorilla gorilla	ENSGGOG00000028110	1 retrocopy	retro_ggor_1916,
Pongo abelii	ENSPPYG00000006895	1 retrocopy	retro_pabe_2280,
Pan troglodytes	ENSPTRG00000007527	1 retrocopy	retro_ptro_1862 ,