RetrogeneDB ID: retro_cjac_3048

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:12513595..12513960(+)
• Located in intron of: ENSCJAG00000011889

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNDC17
• Ensembl ID: ENSCJAG00000011150
• Aliases: None
• Description: thioredoxin domain containing 17 [Source:HGNC Symbol;Acc:28218]

Sequence

>retro_cjac_3048
ATGGCCCACTAAGATGAGGTGAGGGTATCCGGCTTCGGGTTCCACCGGGCCGTGGAGCAGCACAATGGCAAGACCATTTT
CGCCTCCTTTACGGGTTCAAAGGACACCAGAGGGAAAAGCTGGTGCCCCGACTGCATGCAGCCTGAACCAGTCGTACGAG
AGGGGCTGGAGCATGTTCGTGAAGGATGTGTGTTCATCTACTGCCAAGTAGGAGACAAGCCTTATAGGAAAGCTCCAAAT
AATAGCTTCAGAAAAACTGTGATGGTAACAGCAGTGCCTACACTACTCAAGTGTGGAACCCGCCAAAGACTGCTAGAACC
TGAGCGTCTTCAGGCCAACCTGTGGAAACGCTGTTCTCTGAAGAT

Alignment

ORF - retro_cjac_3048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARYEEVSVSGFEEFNRAVKQHNGKTIFAYFTGSKDAGGKSWCPDCVQAEPVVREGLKHVSEGCVFIYCQ
          MA...EV.VSGF..F.RAV.QHNGKTIFA.FTGSKD..GKSWCPDC.Q.EPVVREGL.HV.EGCVFIYCQ
Retrocopy MAH*DEVRVSGFG-FHRAVEQHNGKTIFASFTGSKDTRGKSWCPDCMQPEPVVREGLEHVREGCVFIYCQ

Parental  VGDKPYWKDPNNDFRKNLKVTAVPTLLKYGTPQKLVESECLQANL-VEMLFSED
          VGDKPY.K.PNN.FRK...VTAVPTLLK.GT.Q.L.E.E.LQANL.VE.LFSED
Retrocopy VGDKPYRKAPNNSFRKTVMVTAVPTLLKCGTRQRLLEPERLQANL<VETLFSED

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	0.87 RPM	15.26 RPM
SRP051959_heart	0.11 RPM	5.79 RPM
SRP051959_kidney	0.24 RPM	11.69 RPM
SRP051959_liver	0.41 RPM	10.57 RPM
SRP051959_lung	3.30 RPM	7.14 RPM
SRP051959_lymph_node	6.46 RPM	7.40 RPM
SRP051959_skeletal_muscle	0.11 RPM	5.31 RPM
SRP051959_spleen	2.33 RPM	8.28 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3048 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3048 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3048 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007038	4 retrocopies	retro_amel_1181, retro_amel_1267, retro_amel_148, retro_amel_344,
Callithrix jacchus	ENSCJAG00000011150	4 retrocopies	retro_cjac_2775, retro_cjac_2877, retro_cjac_2887, retro_cjac_3048 ,
Cavia porcellus	ENSCPOG00000002887	1 retrocopy	retro_cpor_116,
Equus caballus	ENSECAG00000025006	1 retrocopy	retro_ecab_430,
Echinops telfairi	ENSETEG00000001905	1 retrocopy	retro_etel_14,
Felis catus	ENSFCAG00000024143	1 retrocopy	retro_fcat_1128,
Homo sapiens	ENSG00000129235	2 retrocopies	retro_hsap_132, retro_hsap_2218,
Gorilla gorilla	ENSGGOG00000003055	2 retrocopies	retro_ggor_1750, retro_ggor_230,
Macropus eugenii	ENSMEUG00000008946	1 retrocopy	retro_meug_1771,
Microcebus murinus	ENSMICG00000006620	2 retrocopies	retro_mmur_1093, retro_mmur_766,
Macaca mulatta	ENSMMUG00000003788	2 retrocopies	retro_mmul_365, retro_mmul_932,
Mustela putorius furo	ENSMPUG00000011338	2 retrocopies	retro_mputfur_518, retro_mputfur_564,
Mus musculus	ENSMUSG00000020803	3 retrocopies	retro_mmus_2817, retro_mmus_2818, retro_mmus_488,
Nomascus leucogenys	ENSNLEG00000009230	2 retrocopies	retro_nleu_2262, retro_nleu_2516,
Oryctolagus cuniculus	ENSOCUG00000016557	1 retrocopy	retro_ocun_297,
Ochotona princeps	ENSOPRG00000000509	2 retrocopies	retro_opri_575, retro_opri_8,
Procavia capensis	ENSPCAG00000003749	1 retrocopy	retro_pcap_180,
Pongo abelii	ENSPPYG00000007880	1 retrocopy	retro_pabe_485,
Pan troglodytes	ENSPTRG00000008644	2 retrocopies	retro_ptro_137, retro_ptro_1683,
Pteropus vampyrus	ENSPVAG00000002399	1 retrocopy	retro_pvam_1187,
Rattus norvegicus	ENSRNOG00000014072	1 retrocopy	retro_rnor_1700,
Sorex araneus	ENSSARG00000006501	1 retrocopy	retro_sara_20,
Ictidomys tridecemlineatus	ENSSTOG00000021986	2 retrocopies	retro_itri_197, retro_itri_574,
Tupaia belangeri	ENSTBEG00000000539	1 retrocopy	retro_tbel_3760,
Tarsius syrichta	ENSTSYG00000010996	2 retrocopies	retro_tsyr_1058, retro_tsyr_982,
Tursiops truncatus	ENSTTRG00000012072	1 retrocopy	retro_ttru_1252,
Vicugna pacos	ENSVPAG00000001554	1 retrocopy	retro_vpac_501,