RetrogeneDB ID: retro_cjac_1664

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:7352006..7352696(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022951
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000031235
• Aliases: None
• Description: None

Sequence

>retro_cjac_1664
GCTCGCGCCACTGGGCCCAGAGTGATGATGGTCGCGCCCTGGACGCGGTTCTACTCCAAAAGCTGCTGCCTGTGCTGCCG
TGTCTGCTTTGGCACCACCCAGCTCGGTGTCTGGTACGCGATCATCAATACTATGGTACTGTTGCTTTTACTGAGTGCCC
CGGCTGATCCGGATCAGGATCACTTTCCGAGTTCTGAAGTGGGAGGTGACTTTGAGTTCACGGATGATGCCACCATGTGC
ATTGCCATTGCGATTTCTCTCCTCATGATCCTGATATGTGCTATGACTAATTACGGAGCATACAAGCAACACGCAGCCCG
GATCGTCCCATTCCTCTGTTACAAGATCTTTGATTTTGCTGTGAACTCCTTGGCTGCAATCGCTGTGCTTGTTTATCCAA
ACTCCATTCAGGAATACATAGGACAACTGCGTGCTAATTTTCCCTGCAGAGATGATGTCACGTCAGTGAATCCTACCTGT
TTGGTCTTCATTATTCTTCTATTTATTAGCATTATCCTGACTTTTAAGGGTTACTTGGTTAGCTGTGTTTGGAACTGCTA
CCTTTACATCAATGGCAGGAACTCCTCAGATGTCCTGGTTTATGTCACCAGCAATGACACTACAGTGCTGCTACCCCCGT
ATGATGATGCCACTGCCAATGGCGCTGCCAAGGAACCTCCGCCACCCTAC

Alignment

ORF - retro_cjac_1664 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 66.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARAAAPAAMKMVAPWTRFYSNSCCLCCHVRTGTILLGVWYLIINAVVLLILLSALADPDQYRFSSSELGG
          ARA..P..M.MVAPWTRFYS.SCCLCC.V..GT..LGVWY.IIN..VLL.LLSA.ADPDQ..F.SSE.GG
Retrocopy ARATGPRVM-MVAPWTRFYSKSCCLCCRVCFGTTQLGVWYAIINTMVLLLLLSAPADPDQDHFPSSEVGG

Parental  DFEFMDDANMCIAIAISVLMILICAMATYGAYKQHAAWIIPFFCYQIFDFALNTLVAITVLVYPNSIQEY
          DFEF.DDA.MCIAIAIS.LMILICAM..YGAYKQHAA.I.PF.CY.IFDFA.N.L.AI.VLVYPNSIQEY
Retrocopy DFEFTDDATMCIAIAISLLMILICAMTNYGAYKQHAARIVPFLCYKIFDFAVNSLAAIAVLVYPNSIQEY

Parental  IRQLPPNFPYRDDVMSVNPTCLVLIILLFISIILTFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDNTV
          I.QL..NFP.RDDV.SVNPTCLV.IILLFISIILTFKGYL.SCVWNCY.YINGRNSSDVLVYVTSND.TV
Retrocopy IGQLRANFPCRDDVTSVNPTCLVFIILLFISIILTFKGYLVSCVWNCYLYINGRNSSDVLVYVTSNDTTV

Parental  LLPPYDEATGNGAAKEPPPPY
          LLPPYD.AT.NGAAKEPPPPY
Retrocopy LLPPYDDATANGAAKEPPPPY

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	0.00 RPM	7.37 RPM
SRP051959_heart	0.00 RPM	30.17 RPM
SRP051959_kidney	0.00 RPM	5.32 RPM
SRP051959_liver	0.00 RPM	2.53 RPM
SRP051959_lung	0.00 RPM	5.64 RPM
SRP051959_lymph_node	0.00 RPM	1.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.03 RPM
SRP051959_spleen	0.00 RPM	4.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1664 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1664 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1664 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786,
Callithrix jacchus	ENSCJAG00000007433	1 retrocopy	retro_cjac_839,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664 , retro_cjac_3027,
Myotis lucifugus	ENSMLUG00000003618	1 retrocopy	retro_mluc_1182,
Macaca mulatta	ENSMMUG00000008926	1 retrocopy	retro_mmul_532,
Mus musculus	ENSMUSG00000022257	1 retrocopy	retro_mmus_1549,
Nomascus leucogenys	ENSNLEG00000003756	1 retrocopy	retro_nleu_1531,
Oryctolagus cuniculus	ENSOCUG00000013689	1 retrocopy	retro_ocun_627,
Otolemur garnettii	ENSOGAG00000000512	3 retrocopies	retro_ogar_1977, retro_ogar_2856, retro_ogar_2902,
Pongo abelii	ENSPPYG00000018771	2 retrocopies	retro_pabe_2311, retro_pabe_279,
Pan troglodytes	ENSPTRG00000020448	1 retrocopy	retro_ptro_546,
Tursiops truncatus	ENSTTRG00000003124	1 retrocopy	retro_ttru_76,