RetrogeneDB ID: retro_pabe_2911

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:142133594..142134992(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC7
• Ensembl ID: ENSPPYG00000008402
• Aliases: None
• Description: dnaJ homolog subfamily C member 7 [Source:RefSeq peptide;Acc:NP_001126143]

Sequence

>retro_pabe_2911
GAAGCAGAGTCTTTGGAGCAACAAGGAAATGCACACTATGCCAAGGAAGATTACAACGAAGCTTATAACTATTAGACAAA
AGCCACAGATATGTGCCCTAAAAATGCTAGCTATCATAGTAATAGAGCAGCTACATTGATGATGCTTGGAAGGTTCTGCG
AAGCCCTTGGAGATACTTTCACAGTCAGTGAAATTGGATGATGGTTTCTTCCGGGGACATCTACGAGAGGGCAAGTGCCA
CCTCTCTCCAGGGAATGCCATGGCAGCACATTGCAGTTTTCAGAGAGCCCTAGAACCGGATCATAACAATGCTCACTCAC
AACAGGAGTTCACAAATGCTAATGCAGTCGAGGAATAGGAGAAAGTCATAGAAACAGGTTTTGAGAAGTGGGCTTTTCAG
AAGGTTGTTTTCTGCATGGACTATGCCCTAGAATTTGCCCCTGTCTGCCATCACTTCAATATCCCTCAAAGCAGAATGTT
TAGCAATGCTGGGTCGTTATCCAGAAGCACAGTCTGTGGCCAGTGACATTTTATGAATGGATTCCACCAATGTGGATGCT
CTGTATGTACGCAGACTTTGCCTTTATTATGAAGATTGTATTGAGTAGGCAGTTGTTCAGTTTTTTGTACAGGCTCTCAG
AATGGCTCCTGACCATGAGAAGGCCTGCCTTGCGTGCAGAAATGCCAGAGCACTTAACGCAAAGAAAGAAGACTGGAATA
AAGCATTTAGGGAAGGAAATTACAAACTAGCTGATGAACTGTACACAGAAGCCCCGGGATAGAGCCCAACAACATAAAAG
CAATTGCTAAACTCTACTGTAACCGGGATATGGTTAATTCCGAGCTTGGGAAATTAGATGATGCAATAGACAGCTGCACA
AATGCAGTGAAGCTCATGACACTTACATAAAAGCCTACTTGAGAAGAGCTCAGTGTTTCATGGACACAGAACAGTATGAA
GAAACAGTGCGAGGCTATGAAAAAAGTATATCAGATGGAGAAAACAAAAGAATACAAACAGCTCCTAAAAAATGCACAGC
TGGAACTGAAGAAGAGTAAGAGGGATAATTACTACAAGGTTCTGGAAGTGGACAAGAATGCCTCTGAGGACAAGATCAAG
AAAGCTTATTGGAAACAGGCCTTGAAGTACCATCCACATCGGCATGATGGAGCCAGTGCTGGAGTTCAAAAGGAGGAGGA
GAAGGTCAAGGAAGTGGCGAGGTCTTTACCATCCTCTTTGATTCCAAGAAAACGATTCGTTATCACAGTGGACAGGACCT
GGATAAGGAAGACATAAATTTGGGTGATTTTGATGCAAACAATATCTTCAAGGTATTCTTCCGCAGTCCTACGGGCTTCA
GCTGTGAAGCATCTGGTCCAAGGATTTTCTTTCTTCAA

Alignment

ORF - retro_pabe_2911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.44 %
• Parental protein coverage: 94.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EAETFKEQGNAYYAKKDYNEAYNYYTKAIDMCPKNASYYGNRAATLMMLGRFREALGDA-QQSVRLDDSF
          EAE....QGNA.YAK.DYNEAYNY.TKA.DMCPKNASY..NRAATLMMLGRF.EALGD...QSV.LDD.F
Retrocopy EAESLEQQGNAHYAKEDYNEAYNY*TKATDMCPKNASYHSNRAATLMMLGRFCEALGDT>SQSVKLDDGF

Parental  VRGHLREGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNANAVMEYEKIAETDFEKRDFRKVVFCM
          .RGHLREGKCHLS.GNAMAA..SFQRALE.DH.NA..QQEF.NANAV.E.EK..ET.FEK..F.KVVFCM
Retrocopy FRGHLREGKCHLSPGNAMAAHCSFQRALEPDHNNAHSQQEFTNANAVEE*EKVIETGFEKWAFQKVVFCM

Parental  DRALEFAPACHRFKI-LKAECLAMLGRYPEAQSVASDILRMDSTNADALYVRGLCLYYEDCIEKA-VQFF
          D.ALEFAP.CH.F.I.LKAECLAMLGRYPEAQSVASDIL.MDSTN.DALYVR.LCLYYEDCIE.A.VQFF
Retrocopy DYALEFAPVCHHFNI>LKAECLAMLGRYPEAQSVASDIL*MDSTNVDALYVRRLCLYYEDCIE*AVVQFF

Parental  VQALRMAPDHEKACIACRNAKALKAKKEDGNKAFKEGNYKLAYELYTEA-LGIDPNNIKTNAKLYCNRGT
          VQALRMAPDHEKAC.ACRNA.AL.AKKED.NKAF.EGNYKLA.ELYTEA..GI.PNNIK..AKLYCNR..
Retrocopy VQALRMAPDHEKACLACRNARALNAKKEDWNKAFREGNYKLADELYTEA<PGIEPNNIKAIAKLYCNRDM

Parental  VNSKLRKLDDAIEDCTNAVKL-DDTYIKAYLRRAQCYMDTEQYEEAVRDYE-KVYQTEKTKEHKQLLKNA
          VNS.L.KLDDAI..CTNAVKL..DTYIKAYLRRAQC.MDTEQYEE.VR.YE.KVYQ.EKTKE.KQLLKNA
Retrocopy VNSELGKLDDAIDSCTNAVKL<HDTYIKAYLRRAQCFMDTEQYEETVRGYE>KVYQMEKTKEYKQLLKNA

Parental  QLELKKSKRKDYYKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEVQKEEEKKFKEV-GEAFTILS
          QLELKKSKR..YYK.L.VDKNASED.IKKAY.K.AL..HP.RH.GASA.VQKEEE.K.KEV.GE.FTIL.
Retrocopy QLELKKSKRDNYYKVLEVDKNASEDKIKKAYWKQALKYHPHRHDGASAGVQKEEE-KVKEV<GEVFTILF

Parental  DPKKKTRYDSGQDLDEEGMNMGDFDPNNIFKAFFGGPGGFSFEASGPGNFFFQ
          D.KK..RY.SGQDLD.E..N.GDFD.NNIFK.FF..P.GFS.EASGP..FF.Q
Retrocopy DSKKTIRYHSGQDLDKEDINLGDFDANNIFKVFFRSPTGFSCEASGPRIFFLQ

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	72.04 RPM
SRP007412_cerebellum	0.00 RPM	61.89 RPM
SRP007412_heart	0.00 RPM	16.44 RPM
SRP007412_kidney	0.00 RPM	43.65 RPM
SRP007412_liver	0.00 RPM	23.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2911 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2911 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3524
Pan troglodytes	retro_ptro_2393
Gorilla gorilla	retro_ggor_2382
Macaca mulatta	retro_mmul_1854

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911 , retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,