RetrogeneDB ID: retro_cjac_2008

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:22871000..22871380(-)
• Located in intron of: ENSCJAG00000015482

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUT
• Ensembl ID: ENSCJAG00000001813
• Aliases: None
• Description: None

Sequence

>retro_cjac_2008
TCACCTTCTCATTCTGCCATGCCCTGCTTTGATAAGACACATGCCATTTCCCCCAGCTAGCAGGCCCAGCCTACAGAGGA
GGGCAGCATGCAGCTCGCTTTGCTCTGCTCTTTGAACACCCCACGGCCTTAACCCAGGGGTCCATGCAGGCTGCTGGCTA
TGACATATTGACCTATGATACAATATCATCCACAGAGAAAGTTCTTGTGAAAATGGACACTCAGATAGCCCTTCCTTCTG
GGTGTTATGGAAGAGTGGCTCCATGGTCTAGTTTAGCTGCAAAACACTTTATAGATGTAGAAGCTGGTGTCAGAGAGAAA
GATTATAGTATAAATGTTGGTGGTATACTGTTCTATTTTGGCAAAGAAAAGTTTGAAGTT

Alignment

ORF - retro_cjac_2008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.92 %
• Parental protein coverage: 50.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPSGSTMPSSEETPAVSPSKRARPAEEGVMQL-RFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEK
          SPS.S.MP....T.A.SPS..A.P.EEG.MQL.RFA.L.EH.TA.T.GS..AAGYD....YD.TI...EK
Retrocopy SPSHSAMPCFDKTHAISPS*QAQPTEEGSMQL<RFALLFEHPTALTQGSMQAAGYDILT-YD-TISSTEK

Parental  ALVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEV
          .LVK.D.QIALPSGCYGRVAP.S.LAAKHFIDV.AGV...DY..NVG..LF.FGKEKFEV
Retrocopy VLVKMDTQIALPSGCYGRVAPWSSLAAKHFIDVEAGVREKDYSINVGGILFYFGKEKFEV

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	0.49 RPM	15.75 RPM
SRP051959_heart	0.25 RPM	3.96 RPM
SRP051959_kidney	0.27 RPM	6.37 RPM
SRP051959_liver	0.32 RPM	5.16 RPM
SRP051959_lung	0.52 RPM	6.38 RPM
SRP051959_lymph_node	0.48 RPM	9.20 RPM
SRP051959_skeletal_muscle	0.09 RPM	3.73 RPM
SRP051959_spleen	0.21 RPM	10.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2008 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2008 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1698
Gorilla gorilla	retro_ggor_1272

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 78 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001873	1 retrocopy	retro_amel_1411,
Bos taurus	ENSBTAG00000011998	3 retrocopies	retro_btau_1765, retro_btau_510, retro_btau_60,
Callithrix jacchus	ENSCJAG00000001813	2 retrocopies	retro_cjac_1014, retro_cjac_2008 ,
Dasypus novemcinctus	ENSDNOG00000024791	8 retrocopies	retro_dnov_204, retro_dnov_2096, retro_dnov_2230, retro_dnov_225, retro_dnov_2270, retro_dnov_2608, retro_dnov_528, retro_dnov_639,
Dipodomys ordii	ENSDORG00000010560	1 retrocopy	retro_dord_146,
Equus caballus	ENSECAG00000015971	1 retrocopy	retro_ecab_375,
Felis catus	ENSFCAG00000015350	3 retrocopies	retro_fcat_1158, retro_fcat_33, retro_fcat_937,
Homo sapiens	ENSG00000128951	6 retrocopies	retro_hsap_1698, retro_hsap_256, retro_hsap_2699, retro_hsap_2963, retro_hsap_3624, retro_hsap_4771,
Gorilla gorilla	ENSGGOG00000005658	5 retrocopies	retro_ggor_1272, retro_ggor_1453, retro_ggor_2053, retro_ggor_2974, retro_ggor_306,
Macropus eugenii	ENSMEUG00000006318	3 retrocopies	retro_meug_1739, retro_meug_2104, retro_meug_476,
Myotis lucifugus	ENSMLUG00000006842	2 retrocopies	retro_mluc_1550, retro_mluc_487,
Macaca mulatta	ENSMMUG00000016898	6 retrocopies	retro_mmul_1429, retro_mmul_2645, retro_mmul_449, retro_mmul_707, retro_mmul_720, retro_mmul_910,
Monodelphis domestica	ENSMODG00000002687	3 retrocopies	retro_mdom_1606, retro_mdom_1858, retro_mdom_693,
Nomascus leucogenys	ENSNLEG00000005996	2 retrocopies	retro_nleu_2602, retro_nleu_859,
Oryctolagus cuniculus	ENSOCUG00000003862	1 retrocopy	retro_ocun_798,
Otolemur garnettii	ENSOGAG00000028847	7 retrocopies	retro_ogar_1207, retro_ogar_1422, retro_ogar_1500, retro_ogar_1653, retro_ogar_2348, retro_ogar_2815, retro_ogar_3485,
Pongo abelii	ENSPPYG00000006454	2 retrocopies	retro_pabe_3820, retro_pabe_3831,
Pan troglodytes	ENSPTRG00000007044	2 retrocopies	retro_ptro_216, retro_ptro_3177,
Rattus norvegicus	ENSRNOG00000007221	1 retrocopy	retro_rnor_859,
Sus scrofa	ENSSSCG00000026096	3 retrocopies	retro_sscr_1121, retro_sscr_122, retro_sscr_175,
Ictidomys tridecemlineatus	ENSSTOG00000007811	1 retrocopy	retro_itri_125,
Tarsius syrichta	ENSTSYG00000012669	9 retrocopies	retro_tsyr_1044, retro_tsyr_1236, retro_tsyr_1251, retro_tsyr_1825, retro_tsyr_1991, retro_tsyr_215, retro_tsyr_616, retro_tsyr_747, retro_tsyr_771,
Tursiops truncatus	ENSTTRG00000015422	2 retrocopies	retro_ttru_1834, retro_ttru_585,
Vicugna pacos	ENSVPAG00000004723	4 retrocopies	retro_vpac_213, retro_vpac_32, retro_vpac_527, retro_vpac_612,