RetrogeneDB ID: retro_cjac_1890

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:19082608..19083061(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LXN
• Ensembl ID: ENSCJAG00000000386
• Aliases: None
• Description: latexin [Source:HGNC Symbol;Acc:13347]

Sequence

>retro_cjac_1890
GCCTTTAAGGGGGCCTCAGTGGCAGACAACTGCCCTGACTACGGCAGGGGACACCCCACAAGGTATTTCAGAGACAGATA
GTCAAGCCAGCACAGAGGATATTCCGGGAAGAGGACCTAAGTGTCACCTCAAACATTCTGTGGAATAAATTATTCTAAAA
TGAGCTGCAGTAAACTGCATATCTCCATCACCTTACCCGGCAGTGGGGCACGAAACTGCACCAGAAATCAACTTCACAAT
TGAGGGAGAAATGGAAAGAGCCTAGATGAAGGAAACAGCACATTTGATCAAAAACTCAAGTCCATGAAGGAAACACTAGA
AGCACAAAATATTCCAGACATTTTGAGAACTGTATCTCCAGAAATGAAGCCAGTTCAACATTCAGCCTGGGTTGCCTGTG
GTTATATAACATGGCAAAATTCTACCAAAAACATGTGGTATAAAAGTGGTAAA

Alignment

ORF - retro_cjac_1890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.26 %
• Parental protein coverage: 68.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASRAALVVQNYINYQQG-TPHRVFQVQKVKEARMEDIPGRGHKYHLKFAIEEIIQNHVMVNCTAEVLYPS
          A...A.V..N...Y..G.TP...........A..EDIPGRG.K.HLK...E.II.....VNC.....YP.
Retrocopy AFKGASVADNCPDYGRG>TPQGISETDS--QASTEDIPGRGPKCHLKHSVE*IILK*AAVNCISPSPYPA

Parental  MGQETVPEVNFTFEGE-TGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVPPEMMLILHLAWVACGYV
          .G.ET.PE.NFT.EGE..GK..DE...TF.Q.LKSMKE.LEAQNIPD....V.PEM....H.AWVACGY.
Retrocopy VGHETAPEINFTIEGE<NGKSLDEGNSTFDQKLKSMKETLEAQNIPDILRTVSPEMKPVQHSAWVACGYI

Parental  IWQNSTEDTWYKMVK
          .WQNST...WYK..K
Retrocopy TWQNSTKNMWYKSGK

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	12.60 RPM
SRP051959_heart	0.00 RPM	4.17 RPM
SRP051959_kidney	0.00 RPM	6.30 RPM
SRP051959_liver	0.17 RPM	3.90 RPM
SRP051959_lung	0.00 RPM	6.72 RPM
SRP051959_lymph_node	0.00 RPM	3.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.80 RPM
SRP051959_spleen	0.00 RPM	5.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1890 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1890 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1890 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009336	2 retrocopies	retro_btau_569, retro_btau_860,
Canis familiaris	ENSCAFG00000009096	1 retrocopy	retro_cfam_1863,
Callithrix jacchus	ENSCJAG00000000386	1 retrocopy	retro_cjac_1890 ,
Homo sapiens	ENSG00000079257	1 retrocopy	retro_hsap_3397,
Gorilla gorilla	ENSGGOG00000003092	1 retrocopy	retro_ggor_2300,
Macaca mulatta	ENSMMUG00000004963	1 retrocopy	retro_mmul_2114,
Nomascus leucogenys	ENSNLEG00000004229	1 retrocopy	retro_nleu_1949,
Pongo abelii	ENSPPYG00000014245	1 retrocopy	retro_pabe_2791,
Pan troglodytes	ENSPTRG00000015571	1 retrocopy	retro_ptro_2308,
Pteropus vampyrus	ENSPVAG00000013608	2 retrocopies	retro_pvam_94, retro_pvam_962,
Tupaia belangeri	ENSTBEG00000017673	3 retrocopies	retro_tbel_2746, retro_tbel_3329, retro_tbel_4516,