RetrogeneDB ID: retro_cjac_1400

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:49271012..49271834(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_1400
ATGGTGGATGGCAGCTTGGAGCAGGCTGACAGGCACATGATCAAGATGGAGGTGGACTACAGTGCCACATGGATCAGCGC
CTACCCATTGTGAGAAGCTGGCCAAGGAAGGAAGACTTCAAGAAGTCATTGAAACCCTTCTCTCTTTGGAGAAGCAGACT
TGTAACTGCTTCCAATATGGTATCTGCATCCCGTATCTTAGTTGCAGTAGTGAAGATGTGCTATGAGGCTAAATAATGGG
ATTTACTTAATGAAAATATGATGCTTTTGTCCAAAAGGCTGAGTAAGTTAAAACAAGCTGCTGCCAAAATGATTCACCAA
TGCTGTACTTATGCTGAGGAAATCACAGACCTTTCTATTAAACTGCAATTCACTGATACTCTAACAAATGGTTACCGAAG
GCGAGATTTATGTTGAAATTGAAAGTGCTCGACTGACTAAAACATTAGCAACTATAAAAGAACAAAATGGTGATGTGAAA
GAGGCAGCCTCTGTTTTACAGGAGCTATAGGTGGAAACCTATGGGTCAATGAAAAAGAAAGAGCAAGCGGAATTTACTTT
GGAGCAAATGAGGCTCTGCCTAGCTGTAAAGGATTACATTCAAACACAAACCAACAGCAAGAAAATTAACACCAAATTTT
TCCAGAAAGAAAATATAGAGAAACTAAAGTTGAAATACTACAATTTAATGATTCAGCTGGATCAACATGATTTGTCTATT
TGCAAGCACTACAGAGCAATATATGATACTCTCTGTATACAGGCAGAAAGTGAAAAATGGCATGGCAGCAGGCTCTGAAG
AGTGTTGTACTATATGTTATCC

Alignment

ORF - retro_cjac_1400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79. %
• Parental protein coverage: 60.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MADGGSERADGRIVKMEVDYSAT-VDQRLP-ECAKLAKEGRLQEVIETLLSLEKQTR-TASDMVSTSRIL
          M.DG..E.AD....KMEVDYSAT..DQRLP..C.KLAKEGRLQEVIETLLSLEKQT..TAS.MVS.SRIL
Retrocopy MVDGSLEQADRHMIKMEVDYSAT<MDQRLP<HCEKLAKEGRLQEVIETLLSLEKQTC>TASNMVSASRIL

Parental  VAVVKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTL-RMVTEGKI
          VAVVKMCYEAK.WDLLNEN.MLLSKR.S.LKQA.AKM..QCCTY.EEITDL.IKL...DTL..MVTEG.I
Retrocopy VAVVKMCYEAK*WDLLNENMMLLSKRLSKLKQAAAKMIHQCCTYAEEITDLSIKLQFTDTL>QMVTEGEI

Parental  YVEIERARLTKTLATIKEQNGDVKEAASILQELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIIS
          YVEIE.ARLTKTLATIKEQNGDVKEAAS.LQEL.VETYGSM.KKE..EF.LEQMRLCLAVKDYI.TQ..S
Retrocopy YVEIESARLTKTLATIKEQNGDVKEAASVLQEL*VETYGSMKKKEQAEFTLEQMRLCLAVKDYIQTQTNS

Parental  KKINTKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVIL
          KKINTKFFQ.EN.EKLKLKYYNLMIQLDQH....LSICKHYRAIYDT.CIQAESEKW.......VLY..L
Retrocopy KKINTKFFQKENIEKLKLKYYNLMIQLDQHD---LSICKHYRAIYDTLCIQAESEKWHGSRL*RVLYYML

Parental  A
          .
Retrocopy S

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	0.00 RPM	11.09 RPM
SRP051959_heart	0.00 RPM	15.03 RPM
SRP051959_kidney	0.00 RPM	12.02 RPM
SRP051959_liver	0.00 RPM	10.38 RPM
SRP051959_lung	0.00 RPM	14.58 RPM
SRP051959_lymph_node	0.00 RPM	10.34 RPM
SRP051959_skeletal_muscle	0.00 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_1400 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1400 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2801
Pan troglodytes	retro_ptro_1898
Gorilla gorilla	retro_ggor_1947

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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,