RetrogeneDB ID: retro_cjac_2635

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:93469181..93469650(-)
• Located in intron of: ENSCJAG00000013924

Retrocopy information

• Ensembl ID: ENSCJAG00000014090
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSCJAG00000020616
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa [Source:HGNC Symbol;Acc:7694]

Sequence

>retro_cjac_2635
ATGGCGTCTCGTATCCTTTCCTCCTGTGTCTGCAGCCTGCCTGCGGCCTTTGCGCCGCTGCCCTGGGTCTCCATGCTGGC
TGCCGCCCAGCCTTTCAGCACCGCCCTGTGCTCTGCGGGGACCCGGACGAGGCCTGGGCCTTCGCAGCCGGCCTCGGTGC
TCGCGCAGGTTCTGGGTAGAGTTACACAGTTGTGCCGCCAGTATTGCGAAGTAATGCCCTTTGACATTAGAGGGCATCCA
GGACCGTGTTCTTTACGTATTGAAGCTCTATGACAAGATTGACCCAGAGAAGCTTTCCGTAAATTCTCATTTTATGAAAG
ACCTGGGCTTAGACAGTTTGGACCAAGTGGAGATTATCATAGCCATGGAAGACGAATTTGGCTTTGAAATTCCTGATTTA
GATGCGGAAAAGTTAATGTGTCCACAAGAAATTGTGGATAACATTGCAGATAAGAAGGATGTATATGAA

Alignment

ORF - retro_cjac_2635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASRVLSFCVRRLPAAFAPLPRVSMLAAAQPFSTALCSAGTRTRPGPSQPASVLAQVPGRVTQLCRQYCE
          MASR.LS.CV..LPAAFAPLP.VSMLAAAQPFSTALCSAGTRTRPGPSQPASVLAQV.GRVTQLCRQYCE
Retrocopy MASRILSSCVCSLPAAFAPLPWVSMLAAAQPFSTALCSAGTRTRPGPSQPASVLAQVLGRVTQLCRQYCE

Parental  AP-PLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDLDAEKLM
          ...PLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEII.AMEDEFGFEIPDLDAEKLM
Retrocopy VM>PLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIIAMEDEFGFEIPDLDAEKLM

Parental  CPQEIVDYIADKKDVYE
          CPQEIVD.IADKKDVYE
Retrocopy CPQEIVDNIADKKDVYE

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	11.03 RPM
SRP051959_heart	0.75 RPM	34.20 RPM
SRP051959_kidney	0.53 RPM	16.99 RPM
SRP051959_liver	0.37 RPM	16.16 RPM
SRP051959_lung	0.57 RPM	7.63 RPM
SRP051959_lymph_node	0.34 RPM	7.15 RPM
SRP051959_skeletal_muscle	0.41 RPM	31.86 RPM
SRP051959_spleen	0.38 RPM	7.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2635 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2635 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Choloepus hoffmanni	ENSCHOG00000003558	2 retrocopies	retro_chof_1517, retro_chof_2498,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635 , retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Dasypus novemcinctus	ENSDNOG00000017122	5 retrocopies	retro_dnov_1450, retro_dnov_1733, retro_dnov_2024, retro_dnov_89, retro_dnov_911,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Homo sapiens	ENSG00000004779	1 retrocopy	retro_hsap_3484,
Gorilla gorilla	ENSGGOG00000006320	1 retrocopy	retro_ggor_2349,
Loxodonta africana	ENSLAFG00000001032	1 retrocopy	retro_lafr_330,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Microcebus murinus	ENSMICG00000007778	2 retrocopies	retro_mmur_1193, retro_mmur_120,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mustela putorius furo	ENSMPUG00000012142	2 retrocopies	retro_mputfur_1135, retro_mputfur_466,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Oryctolagus cuniculus	ENSOCUG00000008457	1 retrocopy	retro_ocun_1712,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Pongo abelii	ENSPPYG00000007192	1 retrocopy	retro_pabe_2879,
Pan troglodytes	ENSPTRG00000007889	1 retrocopy	retro_ptro_2358,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,
Sus scrofa	ENSSSCG00000010795	1 retrocopy	retro_sscr_1017,
Ictidomys tridecemlineatus	ENSSTOG00000024657	2 retrocopies	retro_itri_281, retro_itri_916,
Tursiops truncatus	ENSTTRG00000005258	2 retrocopies	retro_ttru_1229, retro_ttru_989,