RetrogeneDB ID: retro_cjac_1148

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:46124151..46124376(-)
• Located in intron of: ENSCJAG00000004648

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAM16
• Ensembl ID: ENSCJAG00000019772
• Aliases: None
• Description: presequence translocase-associated motor 16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29679]

Sequence

>retro_cjac_1148
CAGTCTTCATTTACTTCCAACCTCTCCAGCATCAGCCTCCAAAAGGCACAGCAGGGTCCCAACATCTCCAAGCTGAGCTT
CAAGAAGGTCCAGAATAACTCTGAATATTTATTCAAGGTGAATGATAAATCCATGTGTGGCTCCTTCTACCTGTAGTCTA
AGGTGCTCTGCTAGAAGGAACCCCAAAATGAGGAAGTCAGAATCCAGGCCCAGGAGGACAGACAG

Alignment

ORF - retro_cjac_1148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64. %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSAAASNLSGLSLQEAQQILNVSKLSPEEVQKNYEHLFKVNDKSVGGSFYLQSKVVRAKERLDEELRIQA
          .S...SNLS..SLQ.AQQ..N.SKLS...VQ.N.E.LFKVNDKS..GSFYL.SKV...KE...EE.RIQA
Retrocopy QSSFTSNLSSISLQKAQQGPNISKLSFKKVQNNSEYLFKVNDKSMCGSFYL*SKVLC*KEPQNEEVRIQA

Parental  QEDRE
          QEDR.
Retrocopy QEDRQ

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	2.11 RPM
SRP051959_heart	0.00 RPM	4.35 RPM
SRP051959_kidney	0.00 RPM	3.19 RPM
SRP051959_liver	0.00 RPM	5.20 RPM
SRP051959_lung	0.02 RPM	2.49 RPM
SRP051959_lymph_node	0.00 RPM	1.71 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.15 RPM
SRP051959_spleen	0.04 RPM	2.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1148 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1148 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148 ,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,