RetrogeneDB ID: retro_cjac_2204

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:184622993..184623974(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034239
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UQCRC1
• Ensembl ID: ENSCJAG00000003132
• Aliases: None
• Description: None

Sequence

>retro_cjac_2204
GCGTCCGTAGTCTGCCGGGCCGCTAGCACCGGGGCACAAGTGCTGCTGCGGACCCCAGCCTTGCGGAGTACGGCAACCTT
CGCTCAGGCGCTCCAGTTTGTGCAGGAGACGCAGGTTAGCAAACTGGACAATGGCCTGCGTGTGGCCTCGGAGCAGTCCT
CCCAGCCCACTTGCACAGTGGGAGTGTGGATTGATGTTGGCAGCCGTTTTGAGACTGAGAAGAACAATGGGGCAGGCTAC
TTTGTGGAGCATCTGGCTTTCAAGGGAACAAAGAATCGGCCTGGCAGTGCCCTGGAGAAGGAGGTGGAGAGCACAGGGGC
GCATCTTAATGCCTGCAGCACCCAGAGCACACAGCTTGCTACATCCAGGCGCTGTCCAAGGATCTGCCAAAAGCTGGGAG
ATCCTGGGTGACACTGTGCAGACCTGTAGTCTGGCAGACTCAGAGATCGAGAAGGAACGTGATGTGATCCTGCAGGAGAT
GCAGGAGAATGATGCCTCCATGCGAGACGTGGTCTTTGACTACCTACATGCCACAGCATTCCAGGGCACGTCTCCAGCCC
AGGCTGTGGAGGGGACCAGTGAGAGTGTCAGGAGGCTGTCTCGTGCAGACTTGACTGAGTACCCCAGCAGGTATTACAGG
GCCCCTCAAATGGTACTGGCAGCGGCGGGAGGAGTGGAGCACCAGCAGCTGTTAGACCTTGCCCAGAAGCACCTGGGTGA
CATCTCTTGGCAGCAGCCGGAGGATGCTGTACCTGCTTTTACTCCATGCCGCTTCACTGACAGTGAGATCCGCCAGCATG
ATGATGCTCTACCTTTAGCCCACATGGCCACTGCAGTAGAGGGTCCTAGCTGAGCCAGCCCAGACAGTGTGGCCTTGCAA
GTGGCCAATGCCAGTATCAGCCACTATGACTGCACTTATGGTGGTGGCGCGCACCTGTCCAGCCACTGGCTTCAATCGTC
GCGGCCAACAAGCTGTGCCAG

Alignment

ORF - retro_cjac_2204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 67.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AQVLLRTSRSPA--LLRTPALRSTATFAQALQFVPETQVSKLDNGLRVASEQSSQPTCTVGVWIDVGSRF
          A.V..R.....A..LLRTPALRSTATFAQALQFV.ETQVSKLDNGLRVASEQSSQPTCTVGVWIDVGSRF
Retrocopy ASVVCRAASTGAQVLLRTPALRSTATFAQALQFVQETQVSKLDNGLRVASEQSSQPTCTVGVWIDVGSRF

Parental  ETEKNNGAGYFVEHLAFKGTKNRPGSTLEKEVESIGAHLNAYSTR-EHTAYYIKALSKDLPKVV-EILGD
          ETEKNNGAGYFVEHLAFKGTKNRPGS.LEKEVES.GAHLNA.ST..EHTA.YI.ALSKDLPK...EILGD
Retrocopy ETEKNNGAGYFVEHLAFKGTKNRPGSALEKEVESTGAHLNACSTQ<EHTACYIQALSKDLPKAG<EILGD

Parental  IVQNCSLEDSQIEKERDVILREMQENDASMRDVVFDYLHATAFQGTSLAQAVEGTSENVRKLSRADLTEY
          .VQ.CSL.DS.IEKERDVIL.EMQENDASMRDVVFDYLHATAFQGTS.AQAVEGTSE.VR.LSRADLTEY
Retrocopy TVQTCSLADSEIEKERDVILQEMQENDASMRDVVFDYLHATAFQGTSPAQAVEGTSESVRRLSRADLTEY

Parental  LSRHYKAPRMVLAAAGGVEHQQLLDLAQKHLGDISWQYPEDAVPAFTPCRFTGSEIRHRDDALPLAHVAI
          .SR.Y.AP.MVLAAAGGVEHQQLLDLAQKHLGDISWQ.PEDAVPAFTPCRFT.SEIR..DDALPLAH.A.
Retrocopy PSRYYRAPQMVLAAAGGVEHQQLLDLAQKHLGDISWQQPEDAVPAFTPCRFTDSEIRQHDDALPLAHMAT

Parental  AVEGPGWANPDNVALQVANAIIGHYDCTYGGGAHLSS-PLASIVAAKKLCQ
          AVEGP..A.PD.VALQVANA.I.HYDCTYGGGAHLSS.PLASIVAA.KLCQ
Retrocopy AVEGPS*ASPDSVALQVANASISHYDCTYGGGAHLSS<PLASIVAANKLCQ

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	66.41 RPM
SRP051959_heart	0.09 RPM	84.02 RPM
SRP051959_kidney	0.07 RPM	66.05 RPM
SRP051959_liver	0.04 RPM	62.77 RPM
SRP051959_lung	0.08 RPM	22.32 RPM
SRP051959_lymph_node	0.09 RPM	21.16 RPM
SRP051959_skeletal_muscle	0.02 RPM	131.51 RPM
SRP051959_spleen	0.06 RPM	22.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2204 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003132	1 retrocopy	retro_cjac_2204 ,
Callithrix jacchus	ENSCJAG00000021200	1 retrocopy	retro_cjac_228,
Mus musculus	ENSMUSG00000025651	1 retrocopy	retro_mmus_473,