RetrogeneDB ID: retro_cjac_3185

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:17315458..17315743(+)
• Located in intron of: ENSCJAG00000000606

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNLRB1
• Ensembl ID: ENSCJAG00000018199
• Aliases: None
• Description: dynein, light chain, roadblock-type 1 [Source:HGNC Symbol;Acc:15468]

Sequence

>retro_cjac_3185
TCAGAGGTGGAGGAGACAATGAAGCAACTTCAGCACCAGAGGAGAGTGCAGAGAATCATCGTGGTGAACACAGGAGGCAT
TCCCATCAAGAGCACCATGGACAACCCCACCAACCACACAGTATGCCAGCCGCATGCACAGCTTCATCCTGAAGGCACAA
AGCATGTGCTCAAAATTGACCCCCAGAATGATCTCACCTTCTGTTGAATTTGCTCCAAGAAAAATGAAATTATGGTTGCA
CCAGACAAAGACTATTTCCTGATTGTGATTCAGAATCCAACCGAA

Alignment

ORF - retro_cjac_3185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.44 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPT-TTQYASLMHSFILKARST-VREIDPQNDLTFL
          .EVEET.K.LQ.Q..VQ.IIVVNT.GIPIKSTMDNPT.TTQYAS.MHSFILKA.S..V..IDPQNDLTF.
Retrocopy SEVEETMKQLQHQRRVQRIIVVNTGGIPIKSTMDNPT>TTQYASRMHSFILKAQSM<VLKIDPQNDLTFC

Parental  RIRSKKNEIMVAPDKDYFLIVIQNPTE
          .I.SKKNEIMVAPDKDYFLIVIQNPTE
Retrocopy *ICSKKNEIMVAPDKDYFLIVIQNPTE

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	0.07 RPM	7.81 RPM
SRP051959_heart	0.05 RPM	6.75 RPM
SRP051959_kidney	0.07 RPM	10.14 RPM
SRP051959_liver	0.04 RPM	6.41 RPM
SRP051959_lung	0.21 RPM	8.85 RPM
SRP051959_lymph_node	0.00 RPM	9.89 RPM
SRP051959_skeletal_muscle	0.04 RPM	4.02 RPM
SRP051959_spleen	0.00 RPM	8.70 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3185 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3185 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_655

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009179	1 retrocopy	retro_amel_1111,
Canis familiaris	ENSCAFG00000007547	6 retrocopies	retro_cfam_1161, retro_cfam_1294, retro_cfam_1577, retro_cfam_1601, retro_cfam_1782, retro_cfam_930,
Callithrix jacchus	ENSCJAG00000018199	10 retrocopies	retro_cjac_1010, retro_cjac_1172, retro_cjac_1274, retro_cjac_1539, retro_cjac_2071, retro_cjac_2902, retro_cjac_3185 , retro_cjac_3215, retro_cjac_3260, retro_cjac_882,
Equus caballus	ENSECAG00000008404	2 retrocopies	retro_ecab_102, retro_ecab_553,
Echinops telfairi	ENSETEG00000018637	2 retrocopies	retro_etel_218, retro_etel_699,
Felis catus	ENSFCAG00000002304	1 retrocopy	retro_fcat_1228,
Homo sapiens	ENSG00000125971	2 retrocopies	retro_hsap_1946, retro_hsap_948,
Gorilla gorilla	ENSGGOG00000023900	1 retrocopy	retro_ggor_764,
Loxodonta africana	ENSLAFG00000029820	2 retrocopies	retro_lafr_722, retro_lafr_852,
Microcebus murinus	ENSMICG00000003253	1 retrocopy	retro_mmur_263,
Myotis lucifugus	ENSMLUG00000004820	3 retrocopies	retro_mluc_1200, retro_mluc_1763, retro_mluc_443,
Macaca mulatta	ENSMMUG00000031253	1 retrocopy	retro_mmul_779,
Nomascus leucogenys	ENSNLEG00000010082	2 retrocopies	retro_nleu_1478, retro_nleu_2456,
Oryctolagus cuniculus	ENSOCUG00000021027	2 retrocopies	retro_ocun_351, retro_ocun_745,
Otolemur garnettii	ENSOGAG00000016802	2 retrocopies	retro_ogar_7, retro_ogar_983,
Ochotona princeps	ENSOPRG00000004714	1 retrocopy	retro_opri_888,
Pongo abelii	ENSPPYG00000010937	1 retrocopy	retro_pabe_810,
Pan troglodytes	ENSPTRG00000013416	1 retrocopy	retro_ptro_655,
Rattus norvegicus	ENSRNOG00000025715	1 retrocopy	retro_rnor_1883,
Ictidomys tridecemlineatus	ENSSTOG00000014820	1 retrocopy	retro_itri_1244,