RetrogeneDB ID: retro_cjac_3911

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286229.1:29126..29591(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011559
• Aliases: None
• Description: None

Sequence

>retro_cjac_3911
ATGTCCAGTGATAGGCAAAGGTCCGATGATGAGAGCCCCAGCACCAGCAGTGGCAGTTCAGATGCGAACCAGCACGACCC
AGCCACTCCAGAGCCTGAAGAACAAGAAGAAAAAAACCTTCTGCCACCCAGCAGAAGAAAAACACCAAGCTCTCTAGCAA
AACCACTGCTAACTTTTCCACTAGTGCTAAAAGAATTCATAAGGAGCTAGCTAAAAATAACCCTTGCTTCTCCTCCTAAT
TGCAGTGCTGGGCCTAAAGGAGATAACATTTATGAATAGAGATCAAGTATACTTGGTCCACCGGGTTCTGTATATGAAGG
TGGTGTCTTTTTTCTGGATATCACGTTTTCATCAGATTATCCATTTAAGCCACCAAAAGTTACTTTCTGCACCAGAATCT
ATTACTGCAACATCAACAGTCAGGGAGTCATCTGTCTGGACATCCTTAAAGACAACTGGAGTCCC

Alignment

ORF - retro_cjac_3911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.81 %
• Parental protein coverage: 74.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSDRQRSDDESPSTSSGSSDADQRDPAAPEPEEQEER-KPSATQQKKNTKLSSKTTAKLSTSAKRIQKE
          MSSDRQRSDDESPSTSSGSSDA.Q.DPA.PEPEEQEE..KPSATQQKKNTKLSSKTTA..STSAKRI.KE
Retrocopy MSSDRQRSDDESPSTSSGSSDANQHDPATPEPEEQEEK<KPSATQQKKNTKLSSKTTANFSTSAKRIHKE

Parental  LAE-ITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSSDYPFKPPKVTFRTRIYHCNI
          LA..ITL..PPNCSAGPKGDNIYE.RS.ILGPPGSVYEGGVFFLDITFSSDYPFKPPKVTF.TRIY.CNI
Retrocopy LAK>ITLASPPNCSAGPKGDNIYE*RSSILGPPGSVYEGGVFFLDITFSSDYPFKPPKVTFCTRIYYCNI

Parental  NSQGVICLDILKDNWSP
          NSQGVICLDILKDNWSP
Retrocopy NSQGVICLDILKDNWSP

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	5.19 RPM
SRP051959_heart	0.00 RPM	7.81 RPM
SRP051959_kidney	0.00 RPM	7.28 RPM
SRP051959_liver	0.00 RPM	3.86 RPM
SRP051959_lung	0.00 RPM	5.61 RPM
SRP051959_lymph_node	0.02 RPM	5.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.92 RPM
SRP051959_spleen	0.00 RPM	6.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3911 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3911 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Choloepus hoffmanni	ENSCHOG00000007325	3 retrocopies	retro_chof_1756, retro_chof_2077, retro_chof_2358,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Callithrix jacchus	ENSCJAG00000007875	4 retrocopies	retro_cjac_1660, retro_cjac_3666, retro_cjac_3882, retro_cjac_925,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911 , retro_cjac_3967,
Callithrix jacchus	ENSCJAG00000015492	3 retrocopies	retro_cjac_512, retro_cjac_657, retro_cjac_791,
Callithrix jacchus	ENSCJAG00000015818	9 retrocopies	retro_cjac_1813, retro_cjac_1815, retro_cjac_1998, retro_cjac_2073, retro_cjac_2511, retro_cjac_2576, retro_cjac_2856, retro_cjac_3174, retro_cjac_3296,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Echinops telfairi	ENSETEG00000019324	2 retrocopies	retro_etel_314, retro_etel_848,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Macaca mulatta	ENSMMUG00000008069	2 retrocopies	retro_mmul_1382, retro_mmul_1834,
Monodelphis domestica	ENSMODG00000010301	2 retrocopies	retro_mdom_1679, retro_mdom_1688,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
Nomascus leucogenys	ENSNLEG00000006290	1 retrocopy	retro_nleu_2068,
Otolemur garnettii	ENSOGAG00000014956	4 retrocopies	retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
Pongo abelii	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Tupaia belangeri	ENSTBEG00000009932	2 retrocopies	retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus	ENSTTRG00000001361	1 retrocopy	retro_ttru_1056,