RetrogeneDB ID: retro_cjac_4022

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL288835.1:22957..23571(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000019583
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HDGF
• Ensembl ID: ENSCJAG00000006157
• Aliases: None
• Description: hepatoma-derived growth factor [Source:HGNC Symbol;Acc:4856]

Sequence

>retro_cjac_4022
ATGTCGCGATCCAACCGGCAGAAGGAATACAAATGCGGGGACCTGGTGTTCGCCAAGATGAAGGGTTACCCACACTGGCC
GGCCTGGATTGACTAGATGCCCGAAGCTGCCGTGAAATCAACAGCCAACAAATACCAAGTCTTTTTTGTCGGGACCTACG
AGACAGCATTCCTGGGCCTCAAAGACCTCTTCCCTTACGAGGAATCCAAGGAGAAGTTTGGCAAGCCCAACAAGAGGAAA
GGGTTCAGCGAGGGGCTGTGGGAGATCGAGAACAACCCTGCCGTCAAGGCTTCTGGCTATCAGTCCTTCCAGAAAAAGAG
CTGCGTGGAAGAGCCTGAACCTGAGCCTGAAGCCACAGAGGGCGACAGTGATAAGAAAAGGAATGCAGAGGGCAGCAGCG
ATGAGGAAGGGAAGCTGGTCATAAACGAGACAGCCAAGGAGAAGAATGAGAAGGGAGCCCTGAAGAGGAGAGCGGGGGAC
CTGCTGGAGGACTCTCCTAAACGTCTCAAGGAGGCAGAAAACTCTGAAGGGGAGGAGAAGGAGGCAGCCATCTTGGAGGG
TGAGAGGCCTCTTCCTGTGAGGTGGAAAAAAATAGCACCCCCTCTGAGCCTGGC

Alignment

ORF - retro_cjac_4022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.72 %
• Parental protein coverage: 85.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSRSNRQKEYKCGDLVFAKMKGYPHWPARIDEMPEAAVKSTANKYQVFFFGTHETAFLGPKDLFPYEESK
          MSRSNRQKEYKCGDLVFAKMKGYPHWPA.ID.MPEAAVKSTANKYQVFF.GT.ETAFLG.KDLFPYEESK
Retrocopy MSRSNRQKEYKCGDLVFAKMKGYPHWPAWID*MPEAAVKSTANKYQVFFVGTYETAFLGLKDLFPYEESK

Parental  EKFGKPNKRKGFSEGLWEIENNPTVKASGYQSSQKKSCVEEPEPEPEATEGDSDKKGNAEGSSDEEGKLV
          EKFGKPNKRKGFSEGLWEIENNP.VKASGYQS.QKKSCVEEPEPEPEATEGDSDKK.NAEGSSDEEGKLV
Retrocopy EKFGKPNKRKGFSEGLWEIENNPAVKASGYQSFQKKSCVEEPEPEPEATEGDSDKKRNAEGSSDEEGKLV

Parental  IDEPAKEKNEKGALKRRAGDLLEDSPKRPKEAENPEEEEKEAATLEGERPLPV-EVEKNSTPSEPG
          I.E.AKEKNEKGALKRRAGDLLEDSPKR.KEAEN.E.EEKEAA.LEGERPLPV.EVEKNSTPSEPG
Retrocopy INETAKEKNEKGALKRRAGDLLEDSPKRLKEAENSEGEEKEAAILEGERPLPV<EVEKNSTPSEPG

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	0.02 RPM	60.46 RPM
SRP051959_heart	0.00 RPM	26.87 RPM
SRP051959_kidney	0.04 RPM	60.72 RPM
SRP051959_liver	0.00 RPM	42.84 RPM
SRP051959_lung	0.00 RPM	29.12 RPM
SRP051959_lymph_node	0.00 RPM	21.30 RPM
SRP051959_skeletal_muscle	0.02 RPM	41.54 RPM
SRP051959_spleen	0.00 RPM	26.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4022 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4022 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039793	1 retrocopy	retro_btau_216,
Callithrix jacchus	ENSCJAG00000006157	2 retrocopies	retro_cjac_338, retro_cjac_4022 ,
Callithrix jacchus	ENSCJAG00000012471	1 retrocopy	retro_cjac_4069,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Dasypus novemcinctus	ENSDNOG00000010231	1 retrocopy	retro_dnov_4,
Equus caballus	ENSECAG00000011178	1 retrocopy	retro_ecab_5,
Echinops telfairi	ENSETEG00000005243	1 retrocopy	retro_etel_1899,
Homo sapiens	ENSG00000143321	1 retrocopy	retro_hsap_33,
Myotis lucifugus	ENSMLUG00000010413	1 retrocopy	retro_mluc_257,
Mus musculus	ENSMUSG00000004897	1 retrocopy	retro_mmus_3647,
Pongo abelii	ENSPPYG00000000703	1 retrocopy	retro_pabe_6,
Pan troglodytes	ENSPTRG00000001474	1 retrocopy	retro_ptro_1,
Sus scrofa	ENSSSCG00000006468	1 retrocopy	retro_sscr_65,