RetrogeneDB ID: retro_cjac_775

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:36452820..36453524(-)
• Located in intron of: ENSCJAG00000020927

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSCJAG00000012010
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_cjac_775
ACCTTGCCAGCTGCCCGGGGAGTCAAGCCGGCACCGGCCTGGAGGCCGGAGGCCTTCACTCCAGACTGGGAAAGCCGAGA
AGTCACCACAGGGACTACTATCACAGCAGTGCAATTTGATGGGGGTGTGGTTCTGGGGACGAATTCCAGAACAACCACTG
GGTCCTACATTGCCAATCGAGTGACTGACAAGCTGACTCCTATTCACGACCACATTTTCTGCTGTCACTCAGGTTCAGCA
GCTGATACCCAGGCAGTAGCTGATGCTGTCACTTACCAGCTTGGTTTCCACAGCACTGAACTGAATGAGCCTCCACTGGT
ACACATAGCAGCCAGCCTGTTTAAGGAGATGTGTTACCAATACAGGGAAGACCTCATGGCAGGAATTATCACCACAGGCT
GAGACCCTCAAGAAGGAGGGCAGGTGTACTCAGTGCCTATGGGGGGTATGATGGTAAGGCAGTCGTTTGCCATTGGAGGC
TTCAGGAGCTCCTACATCTATGGCTATGTTGATGCTACGTACTGGAAAGGCATGACCAAGGAAGAGTGTCTGCAATTCAC
TGCCAATGCTCTCGCTTTGGCCATGGAGCAGGATGGCTCCAGTGGAGAAGTGATCTGCCTGGCAGCCATTGCAGAGTCAG
GGGTAGAGCAGCAAGTACTTTTGGAGACTAGATACCCAAATTCACCATTGCCACTTTACCACCC

Alignment

ORF - retro_cjac_775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.83 %
• Parental protein coverage: 98.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLLAARGVGPAPAWGPEAFTPDWESREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHD
          TL.AARGV.PAPAW.PEAFTPDWESREV.TGTTI.AVQFDGGVVLG..SRTTTGSYIANRVTDKLTPIHD
Retrocopy TLPAARGVKPAPAWRPEAFTPDWESREVTTGTTITAVQFDGGVVLGTNSRTTTGSYIANRVTDKLTPIHD

Parental  HIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQEGG
          HIFCC.SGSAADTQAVADAVTYQLGFHS.ELNEPPLVH.AASLFKEMCY.YREDLMAGII..G.DPQEGG
Retrocopy HIFCCHSGSAADTQAVADAVTYQLGFHSTELNEPPLVHIAASLFKEMCYQYREDLMAGIITTG*DPQEGG

Parental  QVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRLAAI
          QVYSVPMGGMMVRQSFAIGG..SSYIYGYVDATY..GMTKEECLQFTANALALAME.DGSSG.VI.LAAI
Retrocopy QVYSVPMGGMMVRQSFAIGGFRSSYIYGYVDATYWKGMTKEECLQFTANALALAMEQDGSSGEVICLAAI

Parental  AESGVERQVLL-GDQIPKFTIATLPP
          AESGVE.QVLL.GD.IPKFTIATLPP
Retrocopy AESGVEQQVLL<GD*IPKFTIATLPP

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	0.02 RPM	15.38 RPM
SRP051959_heart	0.02 RPM	17.38 RPM
SRP051959_kidney	0.13 RPM	21.45 RPM
SRP051959_liver	0.00 RPM	19.21 RPM
SRP051959_lung	0.05 RPM	10.41 RPM
SRP051959_lymph_node	0.09 RPM	8.74 RPM
SRP051959_skeletal_muscle	0.02 RPM	27.19 RPM
SRP051959_spleen	0.11 RPM	10.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_775 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_775 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_775 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016075	1 retrocopy	retro_amel_1834,
Canis familiaris	ENSCAFG00000015855	1 retrocopy	retro_cfam_2173,
Callithrix jacchus	ENSCJAG00000012010	1 retrocopy	retro_cjac_775 ,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Microcebus murinus	ENSMICG00000014854	2 retrocopies	retro_mmur_140, retro_mmur_718,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Mus musculus	ENSMUSG00000018286	2 retrocopies	retro_mmus_348, retro_mmus_3569,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Tursiops truncatus	ENSTTRG00000000566	1 retrocopy	retro_ttru_405,