RetrogeneDB ID: retro_ptro_35

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:23233150..23235046(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000028313
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSPTRG00000018344
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]

Sequence

>retro_ptro_35
ATGTCCCACTGGGCCCCAGAGTGGAAGAGGGCGGAGGCTAATCCAAGAGACCTTGGGGCCAGCTGGGATGTCAGGGGCAG
CAGAGGCAGTGGCTGGAGAGGCCCCTTCGGCCATCAGGGACCGAGAGCAGCAGGCTCCCGTGAACCACCACTCTGCTTTA
AAATAAAGAACAATATGGTTGGTGCGGTCATTGGTTACAGTGGATCAAAAATAAAAGATCTACAACATTCGACAAACACT
AAAATACAGATCATAAACGGGGAATCTGAAGCAAAAGTCAGAATTTTTGGCAATAGGGAAATGAAAGCAAAGGCCAAAGC
GGCTATAGAAACACTTATTAGAAAACAAGAAAGCTACAACTCAGAATCCAGTGTGGATAATGCTGCATCCCAAACCCCTA
TTGGAAGAAATCTAGGCAGAAATGACATTGTTGGAGAAGCTGAGCCATTGTCAAATTGGGGTCGCATTAGGGCAGCAGTC
GTGGAGCGCGAAAAGAGAAAATGGGCAGATCTACCACCAGTTAAGAAAAACTTTTACATAGAATCCAAAGCAACAAGCTG
GATATCTGAAATGCAGGTGATTAACTGGAGAAAGGAAAATTTCAACATAATGTGTGATGACTTGAAAAGTGGTGAAAAGC
GTCTCATTCCAAACCCAACTTGTAGGCTTCAAGACGCTTTTCAGCAATACCCTGATCTTCTGAAAAGCATAATAAGGGTA
GGGATTGTAAAGCCAACGCCAATTCAGTCACAGGCATGGCCAATTATTCTACAAGGAATAGATCTTATAGAAGTTGCACA
AACCGGAACAGGGAAAACATTGTCCTATCTAATGCCTGGGTTTATTCATCTTGATTCTCAACCAATATCTAGAGAGCAAA
GGAATGGGCCTGGGATGCTAGTCCTTACACCCACTAGAAAGTTGGCTCTTCACGTGGAAGCTGAATGTTCAAAGTATTCA
TATAAAGGTCTTAAAAGCATTTGCGTATATGGTGGTAGAAACAGAAATGGACAAATAGAAGACATTAGCAAAGGTGTAGA
TATCATTATTGCAACTCCTGGGAGGCTGAATGACCTACAAATGAATAACTCTGTCAACCTAAGAAGCATAACCTACTTGG
TTATAGATGAGGCAGATAAAATGCTGGATATGGAATTTGAACCCCAGATAATGAAGATTTTATTAGATGTGCGCCCAGAC
CGACAGACTGTTATGACAAGTGCAACTTGGCCAGATACTGTACGTCAACTAGCACTTTCTTATTTGAAAGATCCTATGAT
GGTTTATGTTGGTAATCTGAATCTAGTGGCTGTAAATACACTGAAGCAAAATATAATTGTTACCACAGAAAAAGAAAAAC
AAGCTCTCACCCAAGAATTCGTAGAGAACATGTCACCCAACGACAAAGTCATCATGTTTGTCAGCCAAAAACATATTGCT
GATGACTTGTCAAGCGACTTCAATATCCAAGGCATATCTGCAGAATCATTACATGGCAACAGTGAACAGAGTGATCGAGA
GCGAGCAGTAGAGGACTTTAAAAGTGGAAACATAAAGATACTGATTACAACTGATATAGTATCCCAAGGTCTTGATCTTA
ATGATGTCACACATGTATATAATTACGATTTCCCAAGGAATATTGACGTATATGTACACAGAGTAGGGTACATTGGACGG
ACAGGAAAGACTGGCACATCAGTTACCCTCATCACTCAGAGAGATTCGAAAATGGCCGGTGAATTGATTAAAATTCTGGA
CAGAGCAAATCAGAGTGTTCCGGAAGATCTTGTAGTAATGGCTGAGCAATACAAGTTAAATCAACAAAAGAGGCACAGAA
AAACACGATCGAGAAAACATGGACAAAGACGCAAGAAGTTTTATTTTTTAAGTTGA

Alignment

ORF - retro_ptro_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.28 %
• Parental protein coverage: 96.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APERRPAEELNRTGPEGYSV--GRGGRWRGPSRPPEAVAAGHEELPLCFALKSHFVGAVIGRGGSKIKNI
          APE...AE...R.......V...RG..WRGP.......AAG..E.PLCF..K...VGAVIG..GSKIK..
Retrocopy APEWKRAEANPRDLGASWDVRGSRGSGWRGPFGHQGPRAAGSREPPLCFKIKNNMVGAVIGYSGSKIKDL

Parental  QSTTNTTIQIIQEQPESLVKIFGSKAMQTKAKAVIDNFVKKLEENYNSECGVDTAFQPSVGKDGSTDNNV
          Q..TNT.IQII....E..V.IFG...M..KAKA.I.....K..E.YNSE..VD.A............N..
Retrocopy QHSTNTKIQIINGESEAKVRIFGNREMKAKAKAAIETLIRK-QESYNSESSVDNAASQTPIGRNLGRNDI

Parental  VAGDRPLIDWDQIREEGLKWQKTKWADLPPIKKNFYKESTATSAMSKVEADSWRKENFNITWDDLKDGEK
          V....PL..W..IR.......K.KWADLPP.KKNFY.ES.ATS..S......WRKENFNI..DDLK.GEK
Retrocopy VGEAEPLSNWGRIRAAVVEREKRKWADLPPVKKNFYIESKATSWISEMQVINWRKENFNIMCDDLKSGEK

Parental  RSIPNPTCTFDDAFQCYPEVMENIKKAGFQKPTPIQSQAWPIVLQGIDLIGVAQTGTGKTLCYLMPGFIH
          R.IPNPTC...DAFQ.YP.....I...G..KPTPIQSQAWPI.LQGIDLI.VAQTGTGKTL.YLMPGFIH
Retrocopy RLIPNPTCRLQDAFQQYPDLLKSIIRVGIVKPTPIQSQAWPIILQGIDLIEVAQTGTGKTLSYLMPGFIH

Parental  LVLQPSLKGQKNRPGMLVLTPTRELALQVEGECCKYSYKGLRSVCVYGGGNRDEQIEELKKGVDIIIATP
          L..QP....Q.N.PGMLVLTPTR.LAL.VE.EC.KYSYKGL.S.CVYGG.NR..QIE...KGVDIIIATP
Retrocopy LDSQPISREQRNGPGMLVLTPTRKLALHVEAECSKYSYKGLKSICVYGGRNRNGQIEDISKGVDIIIATP

Parental  GRLNDLQMSNFVNLKNITYLVLDEADKMLDMGFEPQIMKILLDVRPDRQTVMTTATWPHSVHRLAQSYLK
          GRLNDLQM.N.VNL..ITYLV.DEADKMLDM.FEPQIMKILLDVRPDRQTVMT.ATWP..V..LA.SYLK
Retrocopy GRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIMKILLDVRPDRQTVMTSATWPDTVRQLALSYLK

Parental  EPMIVYVGTLDLVAVSSVKQNIIVTTEEEKWSHMQTFLQNMSSTDKVIVFVSRKAVADHLSSDLILGNIS
          .PM.VYVG.L.LVAV...KQNIIVTTE.EK....Q.F..NMS..DKVI.FVS.K..AD.LSSD.....IS
Retrocopy DPMMVYVGNLNLVAVNTLKQNIIVTTEKEKQALTQEFVENMSPNDKVIMFVSQKHIADDLSSDFNIQGIS

Parental  VESLHGDREQRDREKALENFKTGKVRILIATDLASRGLDVHDVTHVYNFDFPRNIEEYVHRIGRTGRAGR
          .ESLHG..EQ.DRE.A.E.FK.G...ILI.TD..S.GLD..DVTHVYN.DFPRNI..YVHR.G..GR.G.
Retrocopy AESLHGNSEQSDRERAVEDFKSGNIKILITTDIVSQGLDLNDVTHVYNYDFPRNIDVYVHRVGYIGRTGK

Parental  TGVSITTLTRNDWRVASELINILERANQSIPEELVSMAERFKAHQQKREMERKMERPQGRPKKFH
          TG.S.T..T..D...A.ELI.IL.RANQS.PE.LV.MAE..K..QQKR...........R.KKF.
Retrocopy TGTSVTLITQRDSKMAGELIKILDRANQSVPEDLVVMAEQYKLNQQKRHRKTRSRKHGQRRKKFY

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	0.04 RPM	0.02 RPM
SRP007412_cerebellum	0.04 RPM	0.07 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.29 RPM
SRP007412_testis	18.65 RPM	47.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_35 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_35 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_76
Pongo abelii	retro_pabe_39

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007851	1 retrocopy	retro_amel_31,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Equus caballus	ENSECAG00000017971	1 retrocopy	retro_ecab_7,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583,
Homo sapiens	ENSG00000080007	1 retrocopy	retro_hsap_76,
Gorilla gorilla	ENSGGOG00000016092	1 retrocopy	retro_ggor_2889,
Microcebus murinus	ENSMICG00000017145	1 retrocopy	retro_mmur_1603,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14,
Mustela putorius furo	ENSMPUG00000004342	1 retrocopy	retro_mputfur_47,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Oryctolagus cuniculus	ENSOCUG00000006338	2 retrocopies	retro_ocun_1061, retro_ocun_227,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000002562	2 retrocopies	retro_ptro_1536, retro_ptro_1938,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35 ,