RetrogeneDB ID: retro_cjac_2009

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:23108792..23109334(-)
• Located in intron of: ENSCJAG00000015408

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCRB1
• Ensembl ID: ENSCJAG00000017749
• Aliases: None
• Description: zinc finger CCHC-type and RNA binding motif 1 [Source:HGNC Symbol;Acc:29620]

Sequence

>retro_cjac_2009
ATGAGTGGTGAGTTGGCTCCAAGTAAAAGCACAGAGCATATATCCAATTTGCCTATTCCCTGACAATTAATAACTTATAC
TGGATATTTTTCAAGGATGACAAAGTTGTAAAGACTACTATGATGAAATATAAAGATACCAGGAAGAGTAAAGAGGTTGC
ATTTATTTTATTTTTGGATAAAAGAGTTTGTACAAAACAGTATCAGGGCAATAAACAACAGTTACTTGGTAAAGTGATAA
AAGCAAGGAACACAATTGACAACAGAAGAGTAGCTGAGTTCACCCAAAGGCAGGACTACTTTCATGAATTTAAGTGTTAT
ATTTGTGAGAAAAGTGAATAACTAAGTTATGCCTGTCTGAAAAATATGCTTGGAGAACGTGAGCCTCCAAAGAAGAAAGA
AAAAAAGAAAGTTCCTGAACCAGTAGAAGAAACTGAAGCAGAAGCAAGTGAAAGTTAAAGGGAGAATTCTGCTTTTGACA
GCCTTAATCAGGCCATAGCATTCTCGCGAGCCAAAACTGAGTAAGAAAAAAAAGAAGAAAAA

Alignment

ORF - retro_cjac_2009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.43 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGGLAPSKSTVYVSNLP-FSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR
          MSG.LAPSKST...SNLP..SLT.N.LY.IF.K..KVVK.T.MK.KDTRKSK.VAFILFLDK.....CT.
Retrocopy MSGELAPSKSTEHISNLP<YSLTINNLYWIFFKDDKVVKTTMMKYKDTRKSKEVAFILFLDK---RVCTK

Parental  AI--NNKQLFGRVIKASIAIDNGRAAEFIRRRNYFDKSKCYECGESGHLSYACPKNMLGEREPPKKKEKK
          ....N..QL.G.VIKA...IDN.R.AEF..R..YF...KCY.C..S..LSYAC.KNMLGEREPPKKKEKK
Retrocopy QYQGNKQQLLGKVIKARNTIDNRRVAEFTQRQDYFHEFKCYICEKSE*LSYACLKNMLGEREPPKKKEKK

Parental  KKKKAPEPEEEIEEVEESEDEGEDPALDSLSQAIAFQQAKIEEEQKKWK
          K....PEP.EE..E.E.SE...E..A.DSL.QAIAF..AK.E.E.K..K
Retrocopy K---VPEPVEE-TEAEASES*RENSAFDSLNQAIAFSRAKTE*EKKEEK

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	0.51 RPM	5.66 RPM
SRP051959_heart	0.47 RPM	12.40 RPM
SRP051959_kidney	0.16 RPM	13.71 RPM
SRP051959_liver	0.41 RPM	11.00 RPM
SRP051959_lung	0.62 RPM	11.91 RPM
SRP051959_lymph_node	1.12 RPM	13.06 RPM
SRP051959_skeletal_muscle	0.09 RPM	13.04 RPM
SRP051959_spleen	0.67 RPM	12.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2009 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2009 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2009 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019119	2 retrocopies	retro_btau_1637, retro_btau_830,
Choloepus hoffmanni	ENSCHOG00000004490	1 retrocopy	retro_chof_1549,
Callithrix jacchus	ENSCJAG00000017749	3 retrocopies	retro_cjac_2009 , retro_cjac_2662, retro_cjac_4174,
Cavia porcellus	ENSCPOG00000014554	1 retrocopy	retro_cpor_757,
Dasypus novemcinctus	ENSDNOG00000010107	11 retrocopies	retro_dnov_1075, retro_dnov_1120, retro_dnov_1127, retro_dnov_1357, retro_dnov_1599, retro_dnov_1673, retro_dnov_1846, retro_dnov_2146, retro_dnov_2432, retro_dnov_2466, retro_dnov_888,
Equus caballus	ENSECAG00000012174	1 retrocopy	retro_ecab_184,
Erinaceus europaeus	ENSEEUG00000000397	1 retrocopy	retro_eeur_298,
Echinops telfairi	ENSETEG00000019302	1 retrocopy	retro_etel_2080,
Gorilla gorilla	ENSGGOG00000015647	1 retrocopy	retro_ggor_3029,
Loxodonta africana	ENSLAFG00000008847	2 retrocopies	retro_lafr_1183, retro_lafr_783,
Microcebus murinus	ENSMICG00000017422	3 retrocopies	retro_mmur_1236, retro_mmur_236, retro_mmur_466,
Myotis lucifugus	ENSMLUG00000001332	3 retrocopies	retro_mluc_2290, retro_mluc_319, retro_mluc_364,
Monodelphis domestica	ENSMODG00000008893	1 retrocopy	retro_mdom_114,
Mus musculus	ENSMUSG00000022635	1 retrocopy	retro_mmus_847,
Oryctolagus cuniculus	ENSOCUG00000013664	2 retrocopies	retro_ocun_742, retro_ocun_896,
Otolemur garnettii	ENSOGAG00000013178	2 retrocopies	retro_ogar_43, retro_ogar_812,
Ochotona princeps	ENSOPRG00000011095	2 retrocopies	retro_opri_729, retro_opri_927,
Procavia capensis	ENSPCAG00000011749	2 retrocopies	retro_pcap_458, retro_pcap_64,
Pan troglodytes	ENSPTRG00000004838	1 retrocopy	retro_ptro_3231,
Pteropus vampyrus	ENSPVAG00000006651	2 retrocopies	retro_pvam_1343, retro_pvam_697,