RetrogeneDB ID: retro_cjac_3640

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01191212.1:2884..4340(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002199
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSCJAG00000009966
• Aliases: None
• Description: None

Sequence

>retro_cjac_3640
GTTAGAGAAGCGCGGCCATCGTTAGATTGGGATCAAATTAGGGCTAGCGGTCTGGAGAGGGAAAAGAGCAAATGGGCAGA
TTTACCACCAATCAAGAAAAACTTTTACATAGAATCCAAAGCAACAAGCTCCATGTCTGAAATGCAGGTGATTAACTGGA
GAAAGGAAAATTACGATGTAACATGTGATGACTTGAAAAGTGGGGAAAAGCGTCTCATCCCCAAACCTGCTTGTACGTTT
GAAGACGCTTTTCAGCAATACCCTGATCTTTTGAAAAGCATAACAAGGGCAGGATTCAGAAAGCCAACACCAATTCAATC
CCAAGCATGGCCAATTATTCTACAAGGAATAGATCTTATAGGAGTTGCACAAACTGGAACAGGGAAAACGTTGTCCTATT
TAATGCCTGGGTTTATTCATCTTGATTCTCAACCAATATCTAGAGAGCAAAGGAATGGTCCTGGGATGCTGGTTCTTACA
CCCACTAGAGAGTTGGCTGTTCAGGTGGAAGCTGAAAGTTCAAAGTACTCATATAAAGGTCTTAAAAGCATCTGCATATA
TGGTGGTCAAAACAGACAAGAACAAATAGAAGACATTAGCAAAGGTGTAGATATCATTATCGCCACTCCTGGGAGGCTGA
ATTACCTACAGATGAATAATTCTGTCAACCTAAGAAGCGTAACTTATTTAGTTATGGATGAGGCAGATAAAATGCTGGAT
ATGGGATTTGAACCCGAGATAAGGAAGATTTTAATGGATGTGCGCCCAGACCGGCAGACTGTTATGACAAGTGCAACTTG
GCCAGATACTGTTCATCGACTGGCACATTCTTATTTGAAAGATCCTATGATGGTTTATGTTGGTACTCTGAATCTTACGA
CCACAAATACAGTGAAGCAAAATATAATTGTTACCACAGAAAAAGAAAAACGAGCTTTTATCCAATAATTCATAGAGAAC
CTGATGCCAAATGATTCAAGTCATCTTGTTTGTCCACCAAAAATACATTGCTGATGACTTATCAAGTGACTTCAATATCC
AAGGCGTATCTGCAGAAGCACTGCATGGCAACAGAGAACAGAGTGACCAAGAACGAGCATTAGAGGACTTTAAAAGTGGA
AACACAAAGGTACTGATTACAACTGATTTAATAGCCAGAGGCCTTGATATTAATGATGTCACGCATGTATATAATTACGA
TTTCCCATGGAATATAGAAGAATATATCCACAGAGTAGGGCGCACTGGACGGGCAGGAAAGATGGGCACATCAGTTACCC
TCATCACTCAGAGAGATTTAAAAATGGCTAGTGAATTGATTAAAATTCTGGAAAGGACAAATCAGAGTGTTCCGGAAGAT
CTGGTACTAATGGCTGAGCAATACAAGTTAAAACAACAAAAGAGGGACACAGAGAAACGATCAAGAAAAACTGGAGAAAG
ATGCAAGGAGTTTTAC

Alignment

ORF - retro_cjac_3640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.43 %
• Parental protein coverage: 74.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAGARPLIDWDQIREEGLKWQQKKWADLPPIKKNFYKESAATSAMSKVQADSWRKENFNITWDDLKDGEK
          V..ARP..DWDQIR..GL.....KWADLPPIKKNFY.ES.ATS.MS..Q...WRKEN...T.DDLK.GEK
Retrocopy VREARPSLDWDQIRASGLEREKSKWADLPPIKKNFYIESKATSSMSEMQVINWRKENYDVTCDDLKSGEK

Parental  RPIPNPTCTFDDAFHYYPEVMENIKKSGFKKPTPIQAQAWPIVLQGIDLIGVAQTGTGKTLCYLMPGFIH
          R.IP.P.CTF.DAF..YP.....I...GF.KPTPIQ.QAWPI.LQGIDLIGVAQTGTGKTL.YLMPGFIH
Retrocopy RLIPKPACTFEDAFQQYPDLLKSITRAGFRKPTPIQSQAWPIILQGIDLIGVAQTGTGKTLSYLMPGFIH

Parental  LDLQPTFKGQRNRPGMLVLTPTRELALQVEGECCKYSYKGLRSVCVYGGGNRDEQIEELRKGVDIIIATP
          LD.QP....QRN.PGMLVLTPTRELA.QVE.E..KYSYKGL.S.C.YGG.NR.EQIE...KGVDIIIATP
Retrocopy LDSQPISREQRNGPGMLVLTPTRELAVQVEAESSKYSYKGLKSICIYGGQNRQEQIEDISKGVDIIIATP

Parental  GRLNDFQMNNFVNLKNITYLVLDEADRMLDMGFEPQIMKILLDVRPDRQTVMTSATWPRSVHRLAQSYLK
          GRLN..QMNN.VNL...TYLV.DEAD.MLDMGFEP.I.KIL.DVRPDRQTVMTSATWP..VHRLA.SYLK
Retrocopy GRLNYLQMNNSVNLRSVTYLVMDEADKMLDMGFEPEIRKILMDVRPDRQTVMTSATWPDTVHRLAHSYLK

Parental  EPMLVYVGTLDLVAVSSVKQNIIITTEEEKWIHIQTFLQSLSTTD-KVIVFVSRKAVADHLSSELILGNM
          .PM.VYVGTL.L.....VKQNII.TTE.EK...IQ.F...L...D..VI.FV..K..AD.LSS.......
Retrocopy DPMMVYVGTLNLTTTNTVKQNIIVTTEKEKRAFIQ*FIENLMPND>QVILFVHQKYIADDLSSDFNIQGV

Parental  SIESLHGDREQRDREKALENFKTGKVRILIATDLASRGLDVHDITHVYNFDFPRNIEEYVHRIGRTGRAG
          S.E.LHG.REQ.D.E.ALE.FK.G....LI.TDL..RGLD..D.THVYN.DFP.NIEEY.HR.GRTGRAG
Retrocopy SAEALHGNREQSDQERALEDFKSGNTKVLITTDLIARGLDINDVTHVYNYDFPWNIEEYIHRVGRTGRAG

Parental  RTGVSITTMTRNDWRFAPELVNILQRANQIIPDDLLSMAERFKARQQKREMERKMEKPQGRPKKFH
          ..G.S.T..T..D...A.EL..IL.R.NQ..P.DL..MAE..K..QQKR..E....K...R.K.F.
Retrocopy KMGTSVTLITQRDLKMASELIKILERTNQSVPEDLVLMAEQYKLKQQKRDTEKRSRKTGERCKEFY

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
SRP051959_colon	0.04 RPM	0.82 RPM
SRP051959_heart	0.00 RPM	0.63 RPM
SRP051959_kidney	0.02 RPM	0.40 RPM
SRP051959_liver	0.00 RPM	0.41 RPM
SRP051959_lung	0.00 RPM	1.59 RPM
SRP051959_lymph_node	0.00 RPM	0.96 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.26 RPM
SRP051959_spleen	0.00 RPM	1.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3640 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3640 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 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 ,
Callithrix jacchus	ENSCJAG00000012876	1 retrocopy	retro_cjac_1912,
Callithrix jacchus	ENSCJAG00000018844	1 retrocopy	retro_cjac_1298,
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,