RetrogeneDB ID: retro_cjac_1081

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:32688457..32688958(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002841
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2H
• Ensembl ID: ENSCJAG00000010520
• Aliases: None
• Description: None

Sequence

>retro_cjac_1081
AAGCTCATTGAGAGTAAACATGAGGTTACGATCCTGGGAGGACTCAATGAATTTGTAGTGAAGTTTTATGGACCACAAGG
AACACCATATGAAGGCGGTGTATGGAAAGTTAGAGTGGACCTACCTGATAAATACCCTTTCAAATCTCCATCTATAGGAT
TCATGAATAAAATTTTGCATCCCAACATTGATGAAGCGTCAGGAACTCTGTGTCTAGATGTAATTAATCAAACTTGGACA
GCTCTCTATGATCTTACCAATATATTTGAGTCCTTCGGGCCCCAGTTTTTGGCCTATCCTAACCCTATAGATCCTCTCAA
TGGTGACGCTGCAGCCATGTACCTCCACCGACCAGAAGAATACAAGCAGAAAATTAAAGAGTACATCCAGAAATACGCCA
CGGAGGAGGCGCTGAAAGAGCAGGAAGAGGGCACCGGGGACAGCTCATTGGAAAGCTCTATGTCTGACTTTTCCGAAGAT
GAGGCCCAGGATATGGAGTTG

Alignment

ORF - retro_cjac_1081 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.49 %
• Parental protein coverage: 91.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKIFHPNIDEASGTV
          KLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKI.HPNIDEASGT.
Retrocopy KLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKILHPNIDEASGTL

Parental  CLDVINQTWTALYGNDLSDCFKNDGLPRVIVYKGEIDPDEITPNIICVYLARRELTFVEIKQYIQKYATE
          CLDVINQTWTALY..DL...F...G.P....Y...IDP..........YL.R.E.....IK.YIQKYATE
Retrocopy CLDVINQTWTALY--DLTNIFESFG-PQFLAYPNPIDP--LNGDAAAMYLHRPEEYKQKIKEYIQKYATE

Parental  EALKEQEEGTGDSSSESSMSDFSEDEAQDMEL
          EALKEQEEGTGDSS.ESSMSDFSEDEAQDMEL
Retrocopy EALKEQEEGTGDSSLESSMSDFSEDEAQDMEL

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	2.60 RPM	7.08 RPM
SRP051959_heart	3.47 RPM	5.82 RPM
SRP051959_kidney	4.30 RPM	7.70 RPM
SRP051959_liver	2.32 RPM	4.01 RPM
SRP051959_lung	4.28 RPM	6.75 RPM
SRP051959_lymph_node	2.69 RPM	7.44 RPM
SRP051959_skeletal_muscle	2.27 RPM	4.39 RPM
SRP051959_spleen	4.52 RPM	8.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1081 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1081 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1081 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003605	2 retrocopies	retro_chof_1862, retro_chof_1932,
Callithrix jacchus	ENSCJAG00000010520	1 retrocopy	retro_cjac_1081 ,
Homo sapiens	ENSG00000186591	1 retrocopy	retro_hsap_3977,
Nomascus leucogenys	ENSNLEG00000012685	1 retrocopy	retro_nleu_2037,
Pongo abelii	ENSPPYG00000017997	1 retrocopy	retro_pabe_3271,
Rattus norvegicus	ENSRNOG00000048205	2 retrocopies	retro_rnor_2188, retro_rnor_2266,