RetrogeneDB ID: retro_cjac_870

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:97927185..97927534(+)
• Located in intron of: ENSCJAG00000010810

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000037906
• Aliases: None
• Description: None

Sequence

>retro_cjac_870
GGGTATGGTGACTACTCAAAGTTCCTTGACCACTCATAGTAAAAGAGGGATCTATGGTTTGATCTGGACCACCAAGACTT
GAGGTTGAACTGGAGTGAACTGATATACTGGCATCTGAACATATATATCAGGAGCCATGTGGATATGGCCCTCCACACCT
ATTTTTTGGAATATCATGTACAATAATCTCTTCAGCTTCCTGGCTTTCATGAACTTTATGTTATATGTGGAAGGAAATCA
TTCTACCTACCAGTCTGTGGGGCTAAAGCAGTATCCTTTTAATAATCGGTACCTGGGACAAGGCACTGATCCCATCAAAG
AACCTGAGCTGGTGGTTTACTATGAGATA

Alignment

ORF - retro_cjac_870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.43 %
• Parental protein coverage: 62.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GYGDYPKLPDRSQHERDPWYDWDQPDLRLNWGETMHWDIDMYTRNRVDTS-PTPISWDDMCKQLFSFVAF
          GYGDY.K..D.S...RD.W.D.D..DLRLNW.E...W....Y.R..VD....TPI.W..M...LFSF.AF
Retrocopy GYGDYSKFLDHS**KRDLWFDLDHQDLRLNWSELIYWHLNIYIRSHVDMA>STPIFWNIMYNNLFSFLAF

Parental  MVFMFWVGHKYPVYQPVAPKQYPYNDLYLERGGNPSEEPKPVVHYEI
          M.FM..V......YQ.V..KQYP.N..YL..G..P..EP..VV.YEI
Retrocopy MNFMLYVEGNHSTYQSVGLKQYPFNNRYLGQGTDPIKEPELVVYYEI

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	2.48 RPM
SRP051959_heart	0.00 RPM	6.09 RPM
SRP051959_kidney	0.00 RPM	4.88 RPM
SRP051959_liver	0.00 RPM	4.72 RPM
SRP051959_lung	0.00 RPM	2.85 RPM
SRP051959_lymph_node	0.00 RPM	3.95 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.04 RPM
SRP051959_spleen	0.00 RPM	3.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_870 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_870 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_770
Pan troglodytes	retro_ptro_539
Gorilla gorilla	retro_ggor_639
Pongo abelii	retro_pabe_756
Macaca mulatta	retro_mmul_1098

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006651	3 retrocopies	retro_amel_1460, retro_amel_1467, retro_amel_931,
Bos taurus	ENSBTAG00000000091	1 retrocopy	retro_btau_1844,
Canis familiaris	ENSCAFG00000009698	2 retrocopies	retro_cfam_1405, retro_cfam_1947,
Callithrix jacchus	ENSCJAG00000037906	1 retrocopy	retro_cjac_870 ,
Dasypus novemcinctus	ENSDNOG00000003661	1 retrocopy	retro_dnov_65,
Felis catus	ENSFCAG00000006453	2 retrocopies	retro_fcat_501, retro_fcat_856,
Homo sapiens	ENSG00000166136	3 retrocopies	retro_hsap_1363, retro_hsap_1772, retro_hsap_770,
Gorilla gorilla	ENSGGOG00000027239	3 retrocopies	retro_ggor_1062, retro_ggor_2240, retro_ggor_639,
Microcebus murinus	ENSMICG00000001341	1 retrocopy	retro_mmur_859,
Myotis lucifugus	ENSMLUG00000015094	1 retrocopy	retro_mluc_1830,
Macaca mulatta	ENSMMUG00000006636	5 retrocopies	retro_mmul_1098, retro_mmul_1232, retro_mmul_1620, retro_mmul_415, retro_mmul_753,
Monodelphis domestica	ENSMODG00000019356	1 retrocopy	retro_mdom_1543,
Mustela putorius furo	ENSMPUG00000016959	1 retrocopy	retro_mputfur_1259,
Mus musculus	ENSMUSG00000025204	2 retrocopies	retro_mmus_1995, retro_mmus_2909,
Nomascus leucogenys	ENSNLEG00000014774	3 retrocopies	retro_nleu_1068, retro_nleu_2810, retro_nleu_398,
Otolemur garnettii	ENSOGAG00000030711	3 retrocopies	retro_ogar_1237, retro_ogar_152, retro_ogar_2593,
Pongo abelii	ENSPPYG00000002570	3 retrocopies	retro_pabe_1131, retro_pabe_1541, retro_pabe_756,
Pan troglodytes	ENSPTRG00000002851	3 retrocopies	retro_ptro_1186, retro_ptro_539, retro_ptro_936,
Sus scrofa	ENSSSCG00000006166	2 retrocopies	retro_sscr_1092, retro_sscr_444,
Tupaia belangeri	ENSTBEG00000000209	8 retrocopies	retro_tbel_1872, retro_tbel_2950, retro_tbel_3122, retro_tbel_322, retro_tbel_3696, retro_tbel_4042, retro_tbel_4718, retro_tbel_540,