RetrogeneDB ID: retro_cjac_233

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:17917365..17918082(+)
• Located in intron of: ENSCJAG00000005449

Retrocopy information

• Ensembl ID: ENSCJAG00000022320
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007167
• Aliases: None
• Description: None

Sequence

>retro_cjac_233
ATAACCAAGCCATGTGGGGTGCACCTGAGCCGGGAGGTCCTCAAACAGGTAGAGGTCTTCAGGCAGAATCTTTTCCAGGA
GGCTGAGGAATTCCTCCACAGATTCTTGCCACAGAAAATCATATACCTGAATCAGCTCTTGCAAGAGGACTCCCTCAATG
TGGCTGACCTGACTTCCCTCCGAGCCACACTGGACATCCCCATCCCAGATCCTCCACCCAAGGATGATGAGATGGAAACA
GATAAGCAGAAGAAGAAAGAAATCCCTAAGTGTGGATTTCTCCCTGAGAATGAGGTCCTGTCCCTCCTTGCCCTGGTTAA
GTCAGAAGTCTGGACTCCCAAAGAGAAATGCATTCTGGTAATCACATGGATCCAGCACCTGATCCCCAAAATTGAAGACG
GAAATGATTTTGGGGTAGCAATCCAGGAAAAGGTACTGGAGAGGGTGAATGCCGTCAAGACCAAAGTGGAAGCTTTCCAG
ACAACCATTTCCAAGTACTTCTCAGAACATGGGGATGTTGTGGCCAAGGCCTCCAAGGAGACTCATGTGATGGATTACTG
GGCCTCAGTGCACGAGCGAGATGAGGCAGCCTATGGGGAGCTCAGGGCCATGGTGCTGGACCTGAAGGCCTTCTATGCTG
AGCTTTATCATATCATAAGCAGTAACCCGGAGAAAACTGTCAACCCAAAGGGTGAAGAGAAGCCATCTATGTACTGA

Alignment

ORF - retro_cjac_233 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQLLQEDSLNVADLTSLRATLDIPIPD
          ..KPCGV.LS.E..KQVEVFRQNLFQEAEEFL.RFLPQKIIYLNQLLQEDSLNVADLTSLRATLDIPIPD
Retrocopy ITKPCGVHLSREVLKQVEVFRQNLFQEAEEFLHRFLPQKIIYLNQLLQEDSLNVADLTSLRATLDIPIPD

Parental  PPPKDDEMETDKQEKKEVPKCGFLPGNEKVLSLLALVKPEVWTLKEKCILLITWIQHLIPKIEDGNDFGV
          PPPKDDEMETDKQ.KKE.PKCGFLP.NE.VLSLLALVK.EVWT.KEKCIL.ITWIQHLIPKIEDGNDFGV
Retrocopy PPPKDDEMETDKQKKKEIPKCGFLPENE-VLSLLALVKSEVWTPKEKCILVITWIQHLIPKIEDGNDFGV

Parental  AIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVLDLR
          AIQEKVLERVNAVKTKVEAFQTTISKYFSE.GD.VAKASKETHVMDY.A.VHERDEAAYGELRAMVLDL.
Retrocopy AIQEKVLERVNAVKTKVEAFQTTISKYFSEHGDVVAKASKETHVMDYWASVHERDEAAYGELRAMVLDLK

Parental  AFYAELYHIISSNLEKIVNPKGEEKPSMY
          AFYAELYHIISSN.EK.VNPKGEEKPSMY
Retrocopy AFYAELYHIISSNPEKTVNPKGEEKPSMY

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	0.20 RPM	22.41 RPM
SRP051959_heart	0.28 RPM	11.65 RPM
SRP051959_kidney	0.20 RPM	22.45 RPM
SRP051959_liver	0.11 RPM	26.30 RPM
SRP051959_lung	0.70 RPM	21.57 RPM
SRP051959_lymph_node	1.05 RPM	37.97 RPM
SRP051959_skeletal_muscle	0.07 RPM	6.51 RPM
SRP051959_spleen	0.95 RPM	39.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_233 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_233 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233 , retro_cjac_322, retro_cjac_71,
Callithrix jacchus	ENSCJAG00000013111	1 retrocopy	retro_cjac_2307,
Felis catus	ENSFCAG00000005585	1 retrocopy	retro_fcat_1605,
Homo sapiens	ENSG00000100911	4 retrocopies	retro_hsap_1200, retro_hsap_2999, retro_hsap_3033, retro_hsap_3222,
Gorilla gorilla	ENSGGOG00000016025	4 retrocopies	retro_ggor_2078, retro_ggor_2093, retro_ggor_2188, retro_ggor_935,
Myotis lucifugus	ENSMLUG00000009769	1 retrocopy	retro_mluc_2172,
Macaca mulatta	ENSMMUG00000012473	4 retrocopies	retro_mmul_1229, retro_mmul_1919, retro_mmul_1940, retro_mmul_2281,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145,
Nomascus leucogenys	ENSNLEG00000015260	4 retrocopies	retro_nleu_2086, retro_nleu_2726, retro_nleu_3086, retro_nleu_844,
Otolemur garnettii	ENSOGAG00000016584	1 retrocopy	retro_ogar_61,
Pongo abelii	ENSPPYG00000005684	4 retrocopies	retro_pabe_1000, retro_pabe_2486, retro_pabe_2512, retro_pabe_2669,
Pan troglodytes	ENSPTRG00000006196	4 retrocopies	retro_ptro_2028, retro_ptro_2046, retro_ptro_2172, retro_ptro_820,
Sus scrofa	ENSSSCG00000002004	1 retrocopy	retro_sscr_302,