RetrogeneDB ID: retro_cjac_3811

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284745.1:142367..143024(+)
• Located in intron of: ENSCJAG00000010668

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNASEH1
• Ensembl ID: ENSCJAG00000035450
• Aliases: None
• Description: ribonuclease H1 [Source:HGNC Symbol;Acc:18466]

Sequence

>retro_cjac_3811
ATGAGCAGGCTTCTGTTTCTGGCCCACAGAGTCGCCTTGGCCACCGTGCGCTGTCACCCTGCCTATCGTGGGTTCGGGAT
GTTCTATGCCGTGAGAAGGGGCCACAAGACTGGGGTCTTTCTGACCTGGAATGAGTGCAAGGCTCAGGTGGACCGGTTTC
CTGCTGCCAGATTTAAGAAGTTTGCCACAGAGGATGAGGCCTGGGCCTTTGTCAGGAAATCTGCAAGCCCAGAAGCTTCA
GAAGGGCAGAAAAAGCAACATGGACAAGAATCACAGACGAAAGCCAGCAAGCGACTCCATGAGCCACTGGATGCAGATGG
AAATTAAGGCACAGAGCCGTATGCAAAGCACTTGAAGCCCAGTGTGGAGCTGGTGCCTCCAGTTAGCAGAGACATGTTTT
CCTACATGGGAGACTCGGTTGTCGTCTACACAGATGGCTGCTGCTCCAGTAATGGGCAGAGGAGGCCACGAGCAGGAATC
AGCGTTTACTGGGGGCCGGGCCATCCTTTAAATGTAGGCATTAGACTTCCTGGGTGACAGACAAACCAAAGAGCAGAAAT
TCATGCAGCCTGCAAAGCCATTGAACAAGCAAAGGCTCAAAACATCAATAAATTGGTTCTGTATAGAGACAGTATGTTTA
CTATAAATGATATAACT

Alignment

ORF - retro_cjac_3811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.18 %
• Parental protein coverage: 76.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRLLFLAHRVALAAVRCRPASRGFGMFYAVRRGRKTGVFLTWNECKAQVDRFPAARFKKFATEDEAWAF
          MSRLLFLAHRVALA.VRC.PA.RGFGMFYAVRRG.KTGVFLTWNECKAQVDRFPAARFKKFATEDEAWAF
Retrocopy MSRLLFLAHRVALATVRCHPAYRGFGMFYAVRRGHKTGVFLTWNECKAQVDRFPAARFKKFATEDEAWAF

Parental  VRKSASPEASEGQENQHGQESQMKASKRLREPLDGDGDEGAEPYAKHLKPSVEPAPPVSRDLFSYMGDSV
          VRKSASPEASEGQ..QHGQESQ.KASKRL.EPLD.DG..G.EPYAKHLKPSVE..PPVSRD.FSYMGDSV
Retrocopy VRKSASPEASEGQKKQHGQESQTKASKRLHEPLDADGN*GTEPYAKHLKPSVELVPPVSRDMFSYMGDSV

Parental  VVYTDGCCCSNGRRRPRAGIGVYWGPGHLCKNVGIRLPGRQTNQRAEIHAACKAIEQAKAQNISKLVVYT
          VVYTDGCC.SNG.RRPRAGI.VYWGPGH...NVGIRLPG.QTNQRAEIHAACKAIEQAKAQNI.KLV.Y.
Retrocopy VVYTDGCCSSNGQRRPRAGISVYWGPGHPL-NVGIRLPG*QTNQRAEIHAACKAIEQAKAQNINKLVLYR

Parental  DSMFTINGIT
          DSMFTIN.IT
Retrocopy DSMFTINDIT

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	0.71 RPM	6.70 RPM
SRP051959_heart	0.82 RPM	6.98 RPM
SRP051959_kidney	0.91 RPM	8.79 RPM
SRP051959_liver	0.80 RPM	5.81 RPM
SRP051959_lung	0.68 RPM	7.26 RPM
SRP051959_lymph_node	0.71 RPM	8.01 RPM
SRP051959_skeletal_muscle	1.07 RPM	7.86 RPM
SRP051959_spleen	0.80 RPM	8.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3811 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3811 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008547	6 retrocopies	retro_chof_158, retro_chof_1653, retro_chof_1836, retro_chof_2224, retro_chof_485, retro_chof_843,
Callithrix jacchus	ENSCJAG00000035450	1 retrocopy	retro_cjac_3811 ,
Echinops telfairi	ENSETEG00000012674	1 retrocopy	retro_etel_1286,
Homo sapiens	ENSG00000171865	2 retrocopies	retro_hsap_1814, retro_hsap_300,
Gorilla gorilla	ENSGGOG00000034822	2 retrocopies	retro_ggor_2175, retro_ggor_336,
Macropus eugenii	ENSMEUG00000003610	1 retrocopy	retro_meug_1172,
Macaca mulatta	ENSMMUG00000014475	2 retrocopies	retro_mmul_544, retro_mmul_799,
Monodelphis domestica	ENSMODG00000014491	1 retrocopy	retro_mdom_593,
Nomascus leucogenys	ENSNLEG00000015400	2 retrocopies	retro_nleu_2399, retro_nleu_2959,
Pongo abelii	ENSPPYG00000025873	1 retrocopy	retro_pabe_18,
Pan troglodytes	ENSPTRG00000011614	1 retrocopy	retro_ptro_244,
Pteropus vampyrus	ENSPVAG00000002070	1 retrocopy	retro_pvam_144,
Sarcophilus harrisii	ENSSHAG00000013051	1 retrocopy	retro_shar_245,