RetrogeneDB ID: retro_cjac_1169

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:87485559..87485972(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004818
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021388
• Aliases: None
• Description: None

Sequence

>retro_cjac_1169
CCTGGGGACCGTGGCAAGCTGGCCTGGGCCTCAGGGAACTATGCCACCGTTATCTCTCACAACCCTGACACCAAGAAGGC
CCGGATGACGCTGCCCTCTGGCTCCAAGAAGGTTATCTCCTCAGCCAACAGAGCTGCAGTTGGTGTGGTGCCTGGAGGTA
GCCGAATTGACAAACCTATCTTGAAGCCTGACTGGGCCTACCACAAATATAAGGCAAAGAGGAACTGCTGGCCACGAGTA
CAGGGTGTGCCCATGAACTCCGTGGAGCAGCCTTTTGGAGGTGGCAACCACCAGCATGTCACCAAGCCCTCCACCCTCCA
CAGAGATGACGCTGCCGGCCGCATAGTGGGTCTCATTGCTGCCCACGGGACTGGACGTCTCAGGAAACCAAGACTGTGCA
AGAGAAAGAGAAC

Alignment

ORF - retro_cjac_1169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.29 %
• Parental protein coverage: 53.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKY
          PGDRGKLA.ASGNYATVISHNP.TKK.R..LPSGSKKVISSANRA.VGVV.GG.RIDKPILK...AYHKY
Retrocopy PGDRGKLAWASGNYATVISHNPDTKKARMTLPSGSKKVISSANRAAVGVVPGGSRIDKPILKPDWAYHKY

Parental  KAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLR-GTKTVQEKEN
          KAKRNCWPRV.GV.MN.VE.PFGGGNHQH..KPST..RD..AGR.VGLIAA..TGRLR..TKTVQEKEN
Retrocopy KAKRNCWPRVQGVPMNSVEQPFGGGNHQHVTKPSTLHRDDAAGRIVGLIAAHGTGRLR<ETKTVQEKEN

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	0.16 RPM	122.23 RPM
SRP051959_heart	0.00 RPM	100.28 RPM
SRP051959_kidney	0.20 RPM	110.71 RPM
SRP051959_liver	0.09 RPM	130.35 RPM
SRP051959_lung	0.02 RPM	129.60 RPM
SRP051959_lymph_node	0.00 RPM	246.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	140.83 RPM
SRP051959_spleen	0.00 RPM	167.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1169 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1169 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Ailuropoda melanoleuca	ENSAMEG00000005395	1 retrocopy	retro_amel_241,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Canis familiaris	ENSCAFG00000001677	1 retrocopy	retro_cfam_1132,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169 , retro_cjac_1579, retro_cjac_2047,
Cavia porcellus	ENSCPOG00000003854	2 retrocopies	retro_cpor_1006, retro_cpor_1415,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Echinops telfairi	ENSETEG00000007104	4 retrocopies	retro_etel_1100, retro_etel_264, retro_etel_296, retro_etel_916,
Felis catus	ENSFCAG00000026288	1 retrocopy	retro_fcat_570,
Homo sapiens	ENSG00000161016	1 retrocopy	retro_hsap_2851,
Macropus eugenii	ENSMEUG00000013824	9 retrocopies	retro_meug_1116, retro_meug_1354, retro_meug_1757, retro_meug_1817, retro_meug_1881, retro_meug_670, retro_meug_941, retro_meug_960, retro_meug_974,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Monodelphis domestica	ENSMODG00000004283	3 retrocopies	retro_mdom_1055, retro_mdom_1696, retro_mdom_253,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Nomascus leucogenys	ENSNLEG00000010952	2 retrocopies	retro_nleu_1603, retro_nleu_594,
Ornithorhynchus anatinus	ENSOANG00000002646	1 retrocopy	retro_oana_93,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,
Sarcophilus harrisii	ENSSHAG00000013568	2 retrocopies	retro_shar_482, retro_shar_558,
Tursiops truncatus	ENSTTRG00000013858	1 retrocopy	retro_ttru_1147,