RetrogeneDB ID: retro_cjac_4183

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:68480661..68481084(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022848
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008207
• Aliases: None
• Description: None

Sequence

>retro_cjac_4183
ATGTTTGCCTCTGCCAAGCTCGCCTGCACCCCCACTCTGATTCGAGCTGGATTCAGAGTTGCATACAGACCAATTTCCGC
ATCAGTGTTATCTCGACCAGAGACTAGGAATGGAGAGGGCTCTACGGTATTTAATGGGGCCCAGAATGGTGTATCTCAGC
TAATCCAAAGGGAGTTTCAGACCAGTGCAATCAGTAGAGACATTGATACTGCTGCCAAATTTATTGGTGTGGGTGCTGCA
ACAGTAGGAGTGGCTGGTTTTGGTGCTGGTATTGGAACAGTCTTTGGCAGCCTTATTATTGGTTATGCCAGAAACCCTTC
GCTGAAGCAGCAGCTGTTCTCATATGCTATCCTGGGATTTGCCTTGTCTGAAGCTATGGGTCTCTCTTGTTTGATGGTTG
CTTTCTTGATTTTGTTTGTCATG

Alignment

ORF - retro_cjac_4183 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFACAKLACTPALIRAGSRVAYRPISASVLSRPETRNGEGSTVFNGAQNGVSQLIQREFQTSAISRDIDT
          MFA.AKLACTP.LIRAG.RVAYRPISASVLSRPETRNGEGSTVFNGAQNGVSQLIQREFQTSAISRDIDT
Retrocopy MFASAKLACTPTLIRAGFRVAYRPISASVLSRPETRNGEGSTVFNGAQNGVSQLIQREFQTSAISRDIDT

Parental  AAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFA
          AAKFIG.GAATVGVAG.GAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGL.CLMVAFLILF.
Retrocopy AAKFIGVGAATVGVAGFGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLSCLMVAFLILFV

Parental  M
          M
Retrocopy M

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	0.02 RPM	43.18 RPM
SRP051959_heart	0.09 RPM	68.53 RPM
SRP051959_kidney	0.04 RPM	48.57 RPM
SRP051959_liver	0.02 RPM	45.68 RPM
SRP051959_lung	0.02 RPM	11.14 RPM
SRP051959_lymph_node	0.00 RPM	12.12 RPM
SRP051959_skeletal_muscle	0.04 RPM	68.35 RPM
SRP051959_spleen	0.02 RPM	13.38 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4183 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4183 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012367	1 retrocopy	retro_amel_1829,
Bos taurus	ENSBTAG00000002944	1 retrocopy	retro_btau_838,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4, retro_cfam_5,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000007352	7 retrocopies	retro_cjac_1190, retro_cjac_1549, retro_cjac_161, retro_cjac_1878, retro_cjac_289, retro_cjac_4060, retro_cjac_679,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183 ,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070, retro_mdom_295, retro_mdom_545,
Mustela putorius furo	ENSMPUG00000013986	1 retrocopy	retro_mputfur_818,
Oryctolagus cuniculus	ENSOCUG00000012164	1 retrocopy	retro_ocun_949,
Otolemur garnettii	ENSOGAG00000027578	1 retrocopy	retro_ogar_1938,
Rattus norvegicus	ENSRNOG00000001596	1 retrocopy	retro_rnor_1106,
Sorex araneus	ENSSARG00000006733	1 retrocopy	retro_sara_82,
Ictidomys tridecemlineatus	ENSSTOG00000013572	4 retrocopies	retro_itri_1091, retro_itri_1236, retro_itri_324, retro_itri_438,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,
Tursiops truncatus	ENSTTRG00000011524	3 retrocopies	retro_ttru_268, retro_ttru_510, retro_ttru_588,