RetrogeneDB ID: retro_cjac_2404

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:9025500..9025896(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023418
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IFT20
• Ensembl ID: ENSCJAG00000012534
• Aliases: None
• Description: intraflagellar transport 20 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:30989]

Sequence

>retro_cjac_2404
ATGGCCAAGGACATCCTGGGTGAAGCAGGGCTGCACTTCGATGAACTGAACAAGTTGCGGGTGTTGGACCCAGAGGTTAC
CCAGCAAACCATAGAGCTGAAGGAAGAGTGCAAAGACTTTGTGGACAAAATTGGCCAGTTTCAGAAAATAGTTGGTGGTT
TAATTGAGCTTATTGATCAACTTGCAAAAGAAGCAGAAAATGAAAAGATGAAGGCCATCGGTGCTCGGAACTTGCTCAAA
TCTATAGCAAAGCAGAGAGAAGCTCAGCAGCAGCAACTTCAAGCACTAATAGCAGAAAAGAAAATGCAGCTAGAAAGGTA
TCGGGTTGAATATGAAGGTTTATGTAAAGTAGAAGCAGAACAAAATGAATTTATTGACCAATTTATTTTTCAGAAA

Alignment

ORF - retro_cjac_2404 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAKDILGEAGLHFDELNKLRVLDPEVTQQTIELKEECKDFVDKIGQFQKIVGGLIELIDQLAKEAENEKM
          MAKDILGEAGLHFDELNKLRVLDPEVTQQTIELKEECKDFVDKIGQFQKIVGGLIELIDQLAKEAENEKM
Retrocopy MAKDILGEAGLHFDELNKLRVLDPEVTQQTIELKEECKDFVDKIGQFQKIVGGLIELIDQLAKEAENEKM

Parental  KAIGARNLLKSIAKQREAQQQQLQALIAEKKMQLERYRVEYEGLCKVEAEQNEFIDQFIFQK
          KAIGARNLLKSIAKQREAQQQQLQALIAEKKMQLERYRVEYEGLCKVEAEQNEFIDQFIFQK
Retrocopy KAIGARNLLKSIAKQREAQQQQLQALIAEKKMQLERYRVEYEGLCKVEAEQNEFIDQFIFQK

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	5.08 RPM
SRP051959_heart	0.02 RPM	5.47 RPM
SRP051959_kidney	0.16 RPM	8.12 RPM
SRP051959_liver	0.06 RPM	10.14 RPM
SRP051959_lung	0.03 RPM	7.79 RPM
SRP051959_lymph_node	0.02 RPM	7.15 RPM
SRP051959_skeletal_muscle	0.02 RPM	2.71 RPM
SRP051959_spleen	0.00 RPM	7.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2404 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2404 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005111	2 retrocopies	retro_amel_1011, retro_amel_1337,
Bos taurus	ENSBTAG00000008110	1 retrocopy	retro_btau_257,
Callithrix jacchus	ENSCJAG00000012534	2 retrocopies	retro_cjac_2404 , retro_cjac_687,
Cavia porcellus	ENSCPOG00000003153	1 retrocopy	retro_cpor_152,
Echinops telfairi	ENSETEG00000018843	2 retrocopies	retro_etel_1045, retro_etel_1181,
Homo sapiens	ENSG00000109083	1 retrocopy	retro_hsap_1314,
Gorilla gorilla	ENSGGOG00000004568	2 retrocopies	retro_ggor_1026, retro_ggor_1217,
Microcebus murinus	ENSMICG00000005074	1 retrocopy	retro_mmur_987,
Myotis lucifugus	ENSMLUG00000008709	2 retrocopies	retro_mluc_180, retro_mluc_1924,
Macaca mulatta	ENSMMUG00000019143	2 retrocopies	retro_mmul_2165, retro_mmul_2234,
Monodelphis domestica	ENSMODG00000019233	1 retrocopy	retro_mdom_681,
Mustela putorius furo	ENSMPUG00000014353	1 retrocopy	retro_mputfur_247,
Mus musculus	ENSMUSG00000001105	1 retrocopy	retro_mmus_3245,
Nomascus leucogenys	ENSNLEG00000001883	2 retrocopies	retro_nleu_1067, retro_nleu_1941,
Oryctolagus cuniculus	ENSOCUG00000007773	1 retrocopy	retro_ocun_438,
Otolemur garnettii	ENSOGAG00000003333	2 retrocopies	retro_ogar_1169, retro_ogar_72,
Ochotona princeps	ENSOPRG00000005826	6 retrocopies	retro_opri_110, retro_opri_1185, retro_opri_205, retro_opri_293, retro_opri_375, retro_opri_872,
Pongo abelii	ENSPPYG00000008087	2 retrocopies	retro_pabe_1097, retro_pabe_1322,
Sus scrofa	ENSSSCG00000023719	1 retrocopy	retro_sscr_315,
Ictidomys tridecemlineatus	ENSSTOG00000007554	1 retrocopy	retro_itri_713,
Tupaia belangeri	ENSTBEG00000005557	2 retrocopies	retro_tbel_180, retro_tbel_1954,