RetrogeneDB ID: retro_cjac_2950

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:136910803..136911674(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003454
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RRM2
• Ensembl ID: ENSCJAG00000006533
• Aliases: None
• Description: None

Sequence

>retro_cjac_2950
GCCGAGGAGGTTGTGACCACCGAACCGCAGGTGGACCTGTCCAAGGACATTCGGCACTGGGAGTCCCTGAAGCCCGAGGA
GAGATACTTTATATCCCACGTTCTGGCTTTCTTTGCAGCGAGCGATGGCATAGTGAATGAAAACCCGGTGGAGCGATTTA
GCCAAGAAGTTCAGATCACAGAAGCCCGCTGTTTCTATGGCTTCCAAATTGCCATGGAAAACATACATTCTGAAATGTAT
AGTCTCATTGACACTTACATAAAAGATCCCAGGGAAAGGGAATTTCTCTTCAATGCCATTGAAACGATGCCTTGTGTCAA
GAAGAAGGCAGATTGGGCCTTGCGCTGGATTGGGGACAAAGAGGCTACCTATGGTGAACGCGTCGTAGCCTTTGCTGCAG
TGGAAGGCATCTTCTTTTCTGGTTCTTTTGCATCCATATTCTGGCTCAAGAAACGAGGACTGATGCCTAGCCTCATATTT
TCTAATGAACTTATTAGCAGAGAGGAGGGTTTACACTGTGATTTTGCTTGCCTGATGTTCAAACACCTAGGACACAAACC
ATCAGAGGAGAGAGTAAGAAATAATTATCAGTGCTGTTCCGATAGAACAGGAGCTCCTCACTGAGGCCTTGCCTGTGAAG
CTCATTGGGATGAATTGCACTCTAATGAAGCAATACGTTGAGTTTGTAGCAGACAGACTTAAGCTGGAACTGGGTTTTAG
CAAGGTTTTCAGAGTAGAGAATCCATTTGACTTTATGGAGAATATTTCACTGGAAGGAAAGACTAACTTCTTTGAGAAGA
GAGTAGGCGAGCATCAGAGGATGGGAGTGATGTCAAGTCCAACAGAGAATTCTTTTACCTTGGATGCTGAC

Alignment

ORF - retro_cjac_2950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.15 %
• Parental protein coverage: 75.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEASFWTAEEVDLSKDIRHWESLKPEERYFISHVLAFFAASDGIVNENLVERFSQEVQITEARCFYGFQI
          AE....T...VDLSKDIRHWESLKPEERYFISHVLAFFAASDGIVNEN.VERFSQEVQITEARCFYGFQI
Retrocopy AEEVVTTEPQVDLSKDIRHWESLKPEERYFISHVLAFFAASDGIVNENPVERFSQEVQITEARCFYGFQI

Parental  AMENIHSEMYSLLIDTYIKDPSEREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFF
          AMENIHSEMYSL.IDTYIKDP.EREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFF
Retrocopy AMENIHSEMYSL-IDTYIKDPREREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFF

Parental  SGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPSEERVRE-IILNAVRIEQEFLT
          SGSFASIFWLKKRGLMP.L.FSNELISR.EGLHCDFACLMFKHL.HKPSEERVR..II..AV.IEQE.LT
Retrocopy SGSFASIFWLKKRGLMPSLIFSNELISREEGLHCDFACLMFKHLGHKPSEERVRN>II-SAVPIEQELLT

Parental  EALPVKLIGMNCTLMKQYIEFVADRLMLELGFSKVFRVENPFDFMENISLEGKTNFFEKRVGEYQRMGVM
          EALPVKLIGMNCTLMKQY.EFVADRL.LELGFSKVFRVENPFDFMENISLEGKTNFFEKRVGE.QRMGVM
Retrocopy EALPVKLIGMNCTLMKQYVEFVADRLKLELGFSKVFRVENPFDFMENISLEGKTNFFEKRVGEHQRMGVM

Parental  SSPTENSFTLDAD
          SSPTENSFTLDAD
Retrocopy SSPTENSFTLDAD

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	0.04 RPM	14.22 RPM
SRP051959_heart	0.00 RPM	0.12 RPM
SRP051959_kidney	0.04 RPM	3.48 RPM
SRP051959_liver	0.02 RPM	0.82 RPM
SRP051959_lung	0.00 RPM	1.35 RPM
SRP051959_lymph_node	0.02 RPM	5.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.15 RPM	6.28 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2950 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2950 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003409	1 retrocopy	retro_cfam_2113,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950 , retro_cjac_3851,
Callithrix jacchus	ENSCJAG00000015923	1 retrocopy	retro_cjac_4130,
Cavia porcellus	ENSCPOG00000008652	1 retrocopy	retro_cpor_8,
Erinaceus europaeus	ENSEEUG00000009755	2 retrocopies	retro_eeur_421, retro_eeur_585,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640, retro_etel_691,
Homo sapiens	ENSG00000171848	1 retrocopy	retro_hsap_4815,
Macropus eugenii	ENSMEUG00000000121	3 retrocopies	retro_meug_1450, retro_meug_199, retro_meug_277,
Microcebus murinus	ENSMICG00000012789	1 retrocopy	retro_mmur_1384,
Myotis lucifugus	ENSMLUG00000010596	1 retrocopy	retro_mluc_794,
Macaca mulatta	ENSMMUG00000002057	1 retrocopy	retro_mmul_2568,
Monodelphis domestica	ENSMODG00000014763	1 retrocopy	retro_mdom_775,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073,
Nomascus leucogenys	ENSNLEG00000013733	2 retrocopies	retro_nleu_2190, retro_nleu_3040,
Otolemur garnettii	ENSOGAG00000007075	1 retrocopy	retro_ogar_2665,
Pongo abelii	ENSPPYG00000012656	1 retrocopy	retro_pabe_3743,
Rattus norvegicus	ENSRNOG00000023272	1 retrocopy	retro_rnor_331,
Sus scrofa	ENSSSCG00000021742	1 retrocopy	retro_sscr_901,
Tursiops truncatus	ENSTTRG00000017209	1 retrocopy	retro_ttru_603,