RetrogeneDB ID: retro_cjac_2793

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:28373508..28374876(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032940
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMD12
• Ensembl ID: ENSCJAG00000008691
• Aliases: None
• Description: None

Sequence

>retro_cjac_2793
ATGGCGGACGGCGGGTCGGAGTGGGCTGACGGACGCATCATCAAGATGGAGGTGGACTACAGCGCCACGGTGGATCAGCG
CCTACCCGAGTGTGCAAAGCTAGCCAAGGAAGGAAGACTTCATGAAGTCATTGAAACCCTTCTTTCTTTGGAAAAGCAGA
CTCGTACTGCTTCCGATATGGTATCTACAATTCGTATCTTAGTTGAAGTAGTGAAGATGTGCTATGAAGCTAAAGAATGG
GATTTACTTAATGAAAATATTATGCTTTTATCCAAAAGACGGAGTCAGTTAAAACAAGCTGTTGCTAAAATGGTTCAACA
GTGCTGTACTTACGTTGAGGAAATCACAGACCTTCCTATCAAACTTCGATTAATTGATACTCTACGAATGGTCACCGAAG
GCAAGATTTATGTTGAAATTGAGCGTGCTTGACTGACTAAAACAATAGCAACTATAAAAGAACAAAACGGTGATGTGAAA
GAGGCAGCCTCCATCTTGCAGGAGCTACAGGTGGAAACCTACGGGTCAATGGAAAAGAAAGAGAGAGTGGAATTTATTTT
GGAGCAGATGAGGCTCTGCCTAGCTGTGAAGGATTACATTCGAACACAAATCATCAGCAAGAAAATTAACACCAAATTTT
TCCAGGAAGAAAATACAGAGAAATTAAAGTTGAAGTACTATAATTTAATGATTCAGCTGGATCAACATGAGGGATCCTAT
TTGTCTATTTGTAAGCACTACAGAGCAATATATTATACTCCCTGTATACAGGCAGAAAGTGAAAAATGGCAGCAGGCTCT
GAAGAGTGTTGTACTCTATGTTATCCTGGCTCCTTTTGACAACGAACAGTCCGATTTGGTTCACCGAATAAGTGGTGACA
AGAAGTTAGAAGAAATTCCCAAATACAAGGATCTTTTAAAGCTTTTTACCACAATGGAGTTGATGCATTGGTCTACACTT
GTTGAGGACTATGGAATGGAATTAAGAAAAGGTTCCCCTGAGAGTCCTGCAACTGATGTTTTTGGTTCTACAGAGGAAGG
TGAAAAAAGGTGGAAAGACTTGAAGAATAGAGTTGTTGAACATAATATTAGAATAATGGCTAAGTATTATACTTGGATAA
CAATGAAAAGAATGGCACAGCTTCTGGATCTATCTGTTGATGAGTCTGAAGCCTTTCTCTCAAATCTAGTAGTTAACAAG
ACCATCTTTGCTAAAGTAGACAGATTAGCAGGAATTATCAACTTCCAGAGACCCAAGGATCCAAATAATTTATTAAATGA
CTGGTCTCAGAAACTGAACTCATTAATGTCTCTGGTTAACAAAACTACACATCTCATAGCCAAAGAGGAGATGATACATA
ATCTACAA

Alignment

ORF - retro_cjac_2793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDMVSTSRILVAV
          MADGGSE.ADGRI.KMEVDYSATVDQRLPECAKLAKEGRL.EVIETLLSLEKQTRTASDMVST.RILV.V
Retrocopy MADGGSEWADGRIIKMEVDYSATVDQRLPECAKLAKEGRLHEVIETLLSLEKQTRTASDMVSTIRILVEV

Parental  VKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEI
          VKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEI
Retrocopy VKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEI

Parental  ERARLTKTLATIKEQNGDVKEAASILQELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKIN
          ERA.LTKT.ATIKEQNGDVKEAASILQELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKIN
Retrocopy ERA*LTKTIATIKEQNGDVKEAASILQELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKIN

Parental  TKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPFD
          TKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIY.TPCIQAESEKWQQALKSVVLYVILAPFD
Retrocopy TKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYYTPCIQAESEKWQQALKSVVLYVILAPFD

Parental  NEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGSPESPATDVFGSTEEGEKR
          NEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELM.WSTLVEDYGMELRKGSPESPATDVFGSTEEGEKR
Retrocopy NEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMHWSTLVEDYGMELRKGSPESPATDVFGSTEEGEKR

Parental  WKDLKNRVVEHNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPKD
          WKDLKNRVVEHNIRIMAKYYT.ITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPKD
Retrocopy WKDLKNRVVEHNIRIMAKYYTWITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPKD

Parental  PNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
          PNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
Retrocopy PNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ

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	11.09 RPM
SRP051959_heart	0.02 RPM	15.03 RPM
SRP051959_kidney	0.02 RPM	12.02 RPM
SRP051959_liver	0.00 RPM	10.38 RPM
SRP051959_lung	0.02 RPM	14.58 RPM
SRP051959_lymph_node	0.02 RPM	10.34 RPM
SRP051959_skeletal_muscle	0.02 RPM	25.42 RPM
SRP051959_spleen	0.00 RPM	10.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2793 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2793 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008691	2 retrocopies	retro_cjac_1400, retro_cjac_2793 ,
Homo sapiens	ENSG00000197170	1 retrocopy	retro_hsap_2801,
Gorilla gorilla	ENSGGOG00000014761	1 retrocopy	retro_ggor_1947,
Loxodonta africana	ENSLAFG00000010876	1 retrocopy	retro_lafr_467,
Nomascus leucogenys	ENSNLEG00000001265	1 retrocopy	retro_nleu_1541,
Pongo abelii	ENSPPYG00000008565	1 retrocopy	retro_pabe_2223,
Pan troglodytes	ENSPTRG00000022722	1 retrocopy	retro_ptro_1898,
Tupaia belangeri	ENSTBEG00000014760	1 retrocopy	retro_tbel_443,
Tarsius syrichta	ENSTSYG00000013154	1 retrocopy	retro_tsyr_1670,