RetrogeneDB ID: retro_ggor_2889

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:23288213..23290085(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000016424
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSGGOG00000016092
• Aliases: None
• Description: None

Sequence

>retro_ggor_2889
GCCCCAGAGTGGAAGAGGGCTGAGGCTAATCCAAGAGACCTTGGGGCCAGCTGGGATGTCAGGGGCAGCAGAGGCAGTGG
CTGGAGTGGACCCTTCGGCCATCAGGGACCGAGAGCAGCAGGCTCCCGTGAACCACCACTCTGCTTTAAAATAAAGAACA
ATATGGTTGGTGCGGTCATTGGTTACAGTGGATCAAAAATAAAAGATCTACAACATTCGACAAACACTAAAATACAGATC
ATAAACGGGGAATCTGAAGCAAAAGTCAGAATTTTTGGCAATAGGGAAATGAAAGCAAAGGCCAAAGCGGCTATAGAAAC
ACTTATTAGAAAACAAGAAAGCTACAACTCAGAATCCAGTGTGGATAATGCTGCATCCCAAACCCCTATTGGAAGAAATC
TAGGCAGAAATGACATTGTTGGAGAAGCTGAGCCATTGTCAACTTGGGGTCGCATTAGGGCAGCAGTCGTGGAGTGCGAA
AAGAGAAAATGGGCAGATCTACCACCAGTTAAGAAAAACTTTTACATAGAATCCAAAGCAACAAGCTGCATGTCTGAAAT
GCAGGTGATTAACTGGAGAAAGGAAAATTTCAACATAATGTGTGATGACTTGAAAAGTGGTGAAAAGCGTCTCATTCCAA
AACCAACTTGTAGGTTTAAAGACGCTTTTCAGCAATACCCTGATCTTCTGAAAAGCATAATAAGGGTAGGGATTGTAAAG
CCAACACCAATTCAGTCACAGGCATGGCCAATTATTCTACAAGGAATAGATCTTATAGAAGTTGCACAAACCGGAACAGG
GAAAACATTGTCCTATCTAATGCCTGGGTTTATTCATCTTGATTCTCAACCAATATCTAGAGAGCAAAGGAATGGGCCTG
GGATGCTAGTCCTTACACCCACTAGAGAGTTGGCTCTTCACGTGGAAGCTGAATGTTCAAAGTATTCATATAAAGGTCTC
AAAAGCATTTGCATATATGGTGGTAGAAACAGAAATGGACAAATAGAAGACATTAGCAAAGGTGTAGATATCATTATTGC
TACTCCTGGGAGGCTGAATGACCTACAAATGAATAACTCTGTCAACCTAAGAAGCATAACCTACTTGGTTATAGATGAGG
CAGATAAAATGCTGGATATGGAATTTGAACCCCAGATAATGAAGATTTTATTAGATGTGCGCCCAGACCGACAGACTGTT
ATGACAAGTGCAACTTGGCCAGATACTGTACGTCAACTAGCACTTTCTTATTTGAAAGATCCTATGATTGTTTATGTTGG
TAATCTGAATCTAGTGGCTGTAAATACAGTGAAGCAAAATATAATTGTTACCACAGAAAAAGAAAAACGAGCTCTCACCC
AAGAATTCGTAGAGAACATGTCACCCAACAACAAAGTCATCATGTTTGTCAGCCAAAAACATATTGCTGATGACTTGTCA
AGCGACTTCAATATCCAAGGCATATCTGCAGAATCATTACATGGCAACAGTGAACAGAGTGATCAAGAGCGAGCAGTAGA
GGACTTTAAAAGTGGAAACATAAAGATACTGATTACAAATGATATAGTATCCCGAGGTCTTGATCTTAATGGTGTCACAC
ATGTATATAATTACGATTTCCCAAGGAATATTGACGTATATGTACACAGAGTAGGGTACATTGGACGGACAGGAAAGACT
GGCACATCAGTTACCCTCATCACTCAGAGAGATTCGAAAATGGCCGGTGAATTGATTAAAATTCTGGACAGAGCAAATCA
GAGTGTTCCAGAAGATCTTGTAGTAATGGCTGAGCAATACAAGTTAAATCAACAAAAGAGGCACAGAGAAACACGATCAA
GAAAACCTGGACAAAGACGCAAGAAGTTTTAT

Alignment

ORF - retro_ggor_2889 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.16 %
• Parental protein coverage: 96.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APERRPAEELNRRGPEGYSV--GRGSRWSQKSKKSYKVIVGLPRLPLSPSINCHILPIRTGRGGSKIKNI
          APE...AE...R.......V...RGS.WS...........G....PL...I.........G..GSKIK..
Retrocopy APEWKRAEANPRDLGASWDVRGSRGSGWSGPFGHQGPRAAGSREPPLCFKIKNNMVGAVIGYSGSKIKDL

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

Parental  VSGDRPLIDWDQIREEGLKWQKTKWADLPPIKKNFYKESTATSAMSKVEADSWRKENFNITWDDLKDGEK
          V....PL..W..IR.......K.KWADLPP.KKNFY.ES.ATS.MS......WRKENFNI..DDLK.GEK
Retrocopy VGEAEPLSTWGRIRAAVVECEKRKWADLPPVKKNFYIESKATSCMSEMQVINWRKENFNIMCDDLKSGEK

Parental  RPIPNPTCTFDDAFQCYPEVVENIKKAGFQKPTPIQSQAWPIVLQGIDLIGVAQTGTGKTLCYLMPGFIH
          R.IP.PTC.F.DAFQ.YP.....I...G..KPTPIQSQAWPI.LQGIDLI.VAQTGTGKTL.YLMPGFIH
Retrocopy RLIPKPTCRFKDAFQQYPDLLKSIIRVGIVKPTPIQSQAWPIILQGIDLIEVAQTGTGKTLSYLMPGFIH

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

Parental  GRLNDLQMSNFVNLKNITYLVLDEADKMLDMGFEPQIMKILLDVRPDRQTVMTSATWPHSVHRLAQSYLK
          GRLNDLQM.N.VNL..ITYLV.DEADKMLDM.FEPQIMKILLDVRPDRQTVMTSATWP..V..LA.SYLK
Retrocopy GRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIMKILLDVRPDRQTVMTSATWPDTVRQLALSYLK

Parental  EPMIVYVGTLDLVAVSSVKQNIIVTTEEEKWSHMQTFLQNMSSTDKVIVFVSRKAVADHLSSDLILGNIS
          .PMIVYVG.L.LVAV..VKQNIIVTTE.EK....Q.F..NMS...KVI.FVS.K..AD.LSSD.....IS
Retrocopy DPMIVYVGNLNLVAVNTVKQNIIVTTEKEKRALTQEFVENMSPNNKVIMFVSQKHIADDLSSDFNIQGIS

Parental  VESLHGDREQRDREKALENFKTGKVRILIATDLASRGLDVHDVTHVYNFDFPRNIEEYVHRIGRTGRAGR
          .ESLHG..EQ.D.E.A.E.FK.G...ILI..D..SRGLD...VTHVYN.DFPRNI..YVHR.G..GR.G.
Retrocopy AESLHGNSEQSDQERAVEDFKSGNIKILITNDIVSRGLDLNGVTHVYNYDFPRNIDVYVHRVGYIGRTGK

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

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	0.00 RPM
SRP007412_cerebellum	0.12 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	15.44 RPM	41.75 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2889 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_7

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 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	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,