RetrogeneDB ID: retro_hsap_76

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:23018174..23020070(+)
• Located in intron of: ENSG00000233067

Retrocopy information

• Ensembl ID: ENSG00000184735
• Aliases: DDX53, CAGE, CT26
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSG00000080007
• Aliases: DDX43, CT13, HAGE
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]

Sequence

>retro_hsap_76
ATGTCCCACTGGGCCCCAGAGTGGAAGAGGGCGGAGGCTAATCCAAGAGACCTTGGGGCCAGCTGGGATGTCAGGGGCAG
CAGAGGCAGTGGCTGGAGTGGCCCCTTCGGCCATCAGGGACCGAGAGCAGCAGGCTCCCGTGAACCACCACTCTGCTTTA
AAATAAAGAACAATATGGTTGGTGTGGTCATTGGTTACAGTGGATCAAAAATAAAAGATCTACAACATTCGACAAACACT
AAAATACAGATCATAAACGGGGAATCTGAAGCAAAAGTCAGAATTTTTGGCAATAGGGAAATGAAAGCAAAGGCCAAAGC
GGCTATAGAAACACTTATTAGAAAACAAGAAAGCTACAACTCAGAATCCAGTGTGGATAATGCTGCATCCCAAACCCCTA
TTGGAAGAAATCTAGGCAGAAATGACATTGTTGGAGAAGCTGAGCCATTGTCAAATTGGGATCGCATTAGGGCAGCAGTC
GTGGAGTGCGAAAAGAGAAAATGGGCAGATCTACCACCAGTTAAGAAAAACTTTTACATAGAATCCAAAGCAACAAGCTG
CATGTCTGAAATGCAGGTGATTAACTGGAGAAAGGAAAATTTCAACATAACGTGTGATGACTTGAAAAGTGGTGAAAAGC
GTCTCATTCCAAAACCAACTTGCAGGTTTAAAGACGCTTTTCAGCAATACCCTGATCTTCTGAAAAGCATAATAAGGGTA
GGGATTGTAAAGCCAACGCCAATTCAGTCACAGGCATGGCCAATTATTCTACAAGGAATAGATCTTATAGTAGTTGCACA
AACCGGAACAGGGAAAACATTGTCCTATCTAATGCCTGGGTTTATTCATCTTGATTCTCAACCAATATCTAGAGAGCAAA
GGAATGGGCCTGGGATGCTAGTCCTTACACCCACTAGAGAGTTGGCTCTTCACGTGGAAGCTGAATGTTCAAAGTATTCA
TATAAAGGTCTCAAAAGCATTTGCATATATGGTGGTAGAAACAGAAATGGACAAATAGAAGACATTAGCAAAGGTGTAGA
TATCATTATTGCAACTCCTGGGAGGCTGAATGACCTACAAATGAATAACTCTGTCAACCTAAGAAGCATAACCTACTTGG
TTATAGATGAGGCAGATAAAATGCTGGATATGGAATTTGAACCCCAGATAAGGAAGATTTTATTAGATGTGCGCCCAGAC
CGACAGACTGTTATGACAAGTGCAACTTGGCCAGATACTGTACGTCAACTAGCACTTTCTTATTTGAAAGATCCTATGAT
TGTTTATGTTGGTAATCTGAATCTAGTGGCTGTAAATACAGTGAAGCAAAATATAATTGTTACCACAGAAAAAGAAAAAC
GAGCTCTCACCCAAGAATTCGTAGAGAACATGTCACCCAACGACAAAGTCATCATGTTTGTCAGCCAAAAACATATTGCT
GATGACTTGTCAAGCGACTTCAATATCCAAGGCATATCTGCAGAATCATTACATGGCAACAGTGAACAGAGTGATCAAGA
GCGAGCAGTAGAGGACTTTAAAAGCGGAAACATAAAGATACTGATTACAACTGATATAGTATCCCGAGGTCTTGATCTTA
ATGATGTCACACATGTATATAATTATGATTTCCCAAGGAATATTGACGTATATGTACACAGAGTAGGGTACATTGGACGG
ACAGGAAAGACTGGCACATCAGTTACCCTCATCACTCAGAGAGATTCGAAAATGGCCGGTGAATTGATTAAAATTCTGGA
CAGAGCAAATCAGAGTGTTCCGGAAGATCTTGTAGTAATGGCTGAGCAATACAAGTTAAATCAACAAAAGAGGCACAGAG
AAACACGATCAAGAAAACCTGGACAAAGACGCAAGGAGTTTTATTTTTTAAGTTGA

Alignment

ORF - retro_hsap_76 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.6 %
• Parental protein coverage: 96.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APERRPAEELNRTGPEGYSV--GRGGRWRGTSRPPEAVAAGHEELPLCFALKSHFVGAVIGRGGSKIKNI
          APE...AE...R.......V...RG..W.G........AAG..E.PLCF..K...VG.VIG..GSKIK..
Retrocopy APEWKRAEANPRDLGASWDVRGSRGSGWSGPFGHQGPRAAGSREPPLCFKIKNNMVGVVIGYSGSKIKDL

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

Parental  VAGDRPLIDWDQIREEGLKWQKTKWADLPPIKKNFYKESTATSAMSKVEADSWRKENFNITWDDLKDGEK
          V....PL..WD.IR.......K.KWADLPP.KKNFY.ES.ATS.MS......WRKENFNIT.DDLK.GEK
Retrocopy VGEAEPLSNWDRIRAAVVECEKRKWADLPPVKKNFYIESKATSCMSEMQVINWRKENFNITCDDLKSGEK

Parental  RPIPNPTCTFDDAFQCYPEVMENIKKAGFQKPTPIQSQAWPIVLQGIDLIGVAQTGTGKTLCYLMPGFIH
          R.IP.PTC.F.DAFQ.YP.....I...G..KPTPIQSQAWPI.LQGIDLI.VAQTGTGKTL.YLMPGFIH
Retrocopy RLIPKPTCRFKDAFQQYPDLLKSIIRVGIVKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIH

Parental  LVLQPSLKGQRNRPGMLVLTPTRELALQVEGECCKYSYKGLRSVCVYGGGNRDEQIEELKKGVDIIIATP
          L..QP....QRN.PGMLVLTPTRELAL.VE.EC.KYSYKGL.S.C.YGG.NR..QIE...KGVDIIIATP
Retrocopy LDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDISKGVDIIIATP

Parental  GRLNDLQMSNFVNLKNITYLVLDEADKMLDMGFEPQIMKILLDVRPDRQTVMTSATWPHSVHRLAQSYLK
          GRLNDLQM.N.VNL..ITYLV.DEADKMLDM.FEPQI.KILLDVRPDRQTVMTSATWP..V..LA.SYLK
Retrocopy GRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLK

Parental  EPMIVYVGTLDLVAVSSVKQNIIVTTEEEKWSHMQTFLQSMSSTDKVIVFVSRKAVADHLSSDLILGNIS
          .PMIVYVG.L.LVAV..VKQNIIVTTE.EK....Q.F...MS..DKVI.FVS.K..AD.LSSD.....IS
Retrocopy DPMIVYVGNLNLVAVNTVKQNIIVTTEKEKRALTQEFVENMSPNDKVIMFVSQKHIADDLSSDFNIQGIS

Parental  VESLHGDREQRDREKALENFKTGKVRILIATDLASRGLDVHDVTHVYNFDFPRNIEEYVHRIGRTGRAGR
          .ESLHG..EQ.D.E.A.E.FK.G...ILI.TD..SRGLD..DVTHVYN.DFPRNI..YVHR.G..GR.G.
Retrocopy AESLHGNSEQSDQERAVEDFKSGNIKILITTDIVSRGLDLNDVTHVYNYDFPRNIDVYVHRVGYIGRTGK

Parental  TGVSITTLTRNDWRVASELINILERANQSIPEELVSMAERFKAHQQKREMERKMERPQGRPKKFH
          TG.S.T..T..D...A.ELI.IL.RANQS.PE.LV.MAE..K..QQKR..E.....P..R.K.F.
Retrocopy TGTSVTLITQRDSKMAGELIKILDRANQSVPEDLVVMAEQYKLNQQKRHRETRSRKPGQRRKEFY

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
bodymap2_adipose	0.08 RPM	1.13 RPM
bodymap2_adrenal	0.00 RPM	4.24 RPM
bodymap2_brain	0.00 RPM	0.12 RPM
bodymap2_breast	0.00 RPM	1.13 RPM
bodymap2_colon	0.00 RPM	0.23 RPM
bodymap2_heart	0.00 RPM	0.41 RPM
bodymap2_kidney	0.00 RPM	0.27 RPM
bodymap2_liver	0.00 RPM	0.23 RPM
bodymap2_lung	0.00 RPM	0.62 RPM
bodymap2_lymph_node	0.00 RPM	1.43 RPM
bodymap2_ovary	0.00 RPM	0.23 RPM
bodymap2_prostate	0.00 RPM	0.94 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.60 RPM
bodymap2_testis	12.56 RPM	38.52 RPM
bodymap2_thyroid	0.00 RPM	2.96 RPM
bodymap2_white_blood_cells	0.00 RPM	1.22 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_76 was not detected

EST

7 EST(s) were mapped to retro_hsap_76 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BI464283	23018089	23018888	98.3	787	6	771
BI560190	23018089	23018892	98.4	783	8	764
BI560451	23018092	23018722	98.1	627	3	620
CD557286	23018094	23018918	96.7	807	8	780
EL736805	23018174	23018819	99.7	640	2	635
HY032035	23018105	23018516	100	410	0	410
HY216562	23019109	23019542	98.2	428	3	422

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_198970	1787 libraries	25 libraries	14 libraries	2 libraries	1 library

The graphical summary, for retro_hsap_76 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_76 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_76 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_35
Pongo abelii	retro_pabe_39

---

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 ,
Homo sapiens	ENSG00000107625	2 retrocopies	retro_hsap_2089, retro_hsap_2866,
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	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,