RetrogeneDB ID: retro_cjac_1597

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:43244079..43245256(-)
• Located in intron of: ENSCJAG00000003018

Retrocopy information

• Ensembl ID: ENSCJAG00000003024
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSCJAG00000011185
• Aliases: None
• Description: None

Sequence

>retro_cjac_1597
ATGGCACTGAAGGTAGCAACAGCCTCTGGCGGCGCTATGAAGGCAGTGCTCCGGCCAGCCCTTCTGTGAAGTGCCTGGGA
GGTTCTAGGTGCCCATGAGGCCCCCCTCGAAGAGCATCTCCTCACAACAAATGATTCCTCCATCAGCTAAGTATGGCGGG
CGGCACACATCGACCGTGATCCCTGGTGATGGCATCGGGCCAAAGCTCATGCTGCATGTGAAGTCTGTTTTCAGGCACGC
CTGTGTCGGGTGGACTTTGAAGAGGTGCACGTGAGTTCCAACCTTGATGAAGAAGACATTAGCAAAGCCATCATGGCCAT
CCGCCGGAACCATGTGGCCCCGAAGGGCAATATCAACACCAACCGTAATCTGCCACCATCCCACAAATCCCGAAACAACA
TCTTCCGCACCAGCCCGGACCTCTATGCCAACGTCATCCACTATAAGAGCCTGCCAGGTGTGGTGACCCGACACAAGGAC
ATAGACATCCTCATTGTCCGGGAGAACACGGAGGGTGAGTACAGCAGCCTGGAGCATGAGAGTGTGGCGGGAGTGGTGGA
GAGCCTGAAGATCATCACCAAGGCCAAGTCCCTACGCGTTGCCATATGCTTTCAAGCTGGCGCTGAAGAGCGGGCGCAAG
AAAGTGACGGCCATGTACAAGGCCAACATCATGAAACTGGGCAACAGGCTCTTCCTCCAATGCTGCAGGGAGGTAGCAGC
TGGTTACCCCCAGATCACTTTCAAGAACACGATTGTGGACAACACCACCATGCAGCTGGTGTCCTGGCCCCAGCAATTTG
ATGTCGTGGTGATGCCCAATCTCTATGGCAACCTGGTCAGCAATGTCTGCTCAGGACTGGTCGGAGGCCCAGGCCTTGTG
GCTGGGGCCAACTATGGCCATGTGTACACGGTGTTTGAAACAGCTACGAGGAACACTGGCAAGAGTATCGCCAATAAGAA
CATCGCCAACCCCACAGCCATCCTGCTGGCCAGCTGCATGATGCTGGATCACCTCAAGCTGCACTTCTACGCCACCTCCA
TCCGTAAGGCTGTCCTGGTGTCCATGGACAATGAGAATATGCACACTCCAGACATTGGGGGCCAGGGCATAACATCTGAG
GCCATCCAGGACATCATCAGCCACATCCGTGTCATCAATGGCCAGGCTGTGGAGGCC

Alignment

ORF - retro_cjac_1597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALKVATAASGAAKAVLRPALFCRPWEVLGAYEAP-SRSSSSQQTIPPSAKYGGRHTVTMIPGDGIGPEL
          MALKVATA..GA.KAVLRPAL....WEVLGA.EAP.S.S.SSQQ.IPPSAKYGGRHT.T.IPGDGIGP.L
Retrocopy MALKVATASGGAMKAVLRPALL*SAWEVLGAHEAP>SKSISSQQMIPPSAKYGGRHTSTVIPGDGIGPKL

Parental  MLHVKSVFRHACVP-VDFEEVHVSSNADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTS
          MLHVKSVFRHACV..VDFEEVHVSSN.DEEDI..AIMAIRRN.VA.KGNI.TN.NLPPSHKSRNNI.RTS
Retrocopy MLHVKSVFRHACVG<VDFEEVHVSSNLDEEDISKAIMAIRRNHVAPKGNINTNRNLPPSHKSRNNIFRTS

Parental  LDLYANVIHCKSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLA
          .DLYANVIH.KSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLR.A...F...
Retrocopy PDLYANVIHYKSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRVA-ICFQAG

Parental  QE-SGRKKVTAVHKANIMKLGDGLFLQCCREVAAGYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYG
          .E.SGRKKVTA..KANIMKLG..LFLQCCREVAAGYPQITF.N.IVDNTTMQLVS.PQQFDV.VMPNLYG
Retrocopy AE>SGRKKVTAMYKANIMKLGNRLFLQCCREVAAGYPQITFKNTIVDNTTMQLVSWPQQFDVVVMPNLYG

Parental  NIVNNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATS
          N.V.NVC.GLVGGPGLVAGANYGHVY.VFETATRNTGKSIANKNIANPTA.LLASCMMLDHLKLH.YATS
Retrocopy NLVSNVCSGLVGGPGLVAGANYGHVYTVFETATRNTGKSIANKNIANPTAILLASCMMLDHLKLHFYATS

Parental  IRKAVLASMDNENMHTPDIGGQGTTSEAIQDIIRHIRVVNGRAVEA
          IRKAVL.SMDNENMHTPDIGGQG.TSEAIQDII.HIRV.NG.AVEA
Retrocopy IRKAVLVSMDNENMHTPDIGGQGITSEAIQDIISHIRVINGQAVEA

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	0.09 RPM	16.22 RPM
SRP051959_heart	0.18 RPM	30.52 RPM
SRP051959_kidney	0.00 RPM	35.30 RPM
SRP051959_liver	0.09 RPM	10.98 RPM
SRP051959_lung	0.39 RPM	15.31 RPM
SRP051959_lymph_node	0.00 RPM	15.43 RPM
SRP051959_skeletal_muscle	0.02 RPM	33.67 RPM
SRP051959_spleen	0.67 RPM	17.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1597 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1597 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1597 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018466	1 retrocopy	retro_amel_1892,
Bos taurus	ENSBTAG00000001059	1 retrocopy	retro_btau_1194,
Canis familiaris	ENSCAFG00000019286	1 retrocopy	retro_cfam_1023,
Callithrix jacchus	ENSCJAG00000011185	1 retrocopy	retro_cjac_1597 ,
Equus caballus	ENSECAG00000018509	1 retrocopy	retro_ecab_941,
Homo sapiens	ENSG00000067829	1 retrocopy	retro_hsap_759,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Loxodonta africana	ENSLAFG00000006904	1 retrocopy	retro_lafr_560,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Mustela putorius furo	ENSMPUG00000008781	1 retrocopy	retro_mputfur_644,
Mus musculus	ENSMUSG00000002010	1 retrocopy	retro_mmus_134,
Nomascus leucogenys	ENSNLEG00000013540	1 retrocopy	retro_nleu_394,
Otolemur garnettii	ENSOGAG00000006735	1 retrocopy	retro_ogar_25,
Pteropus vampyrus	ENSPVAG00000013163	1 retrocopy	retro_pvam_373,
Rattus norvegicus	ENSRNOG00000037284	1 retrocopy	retro_rnor_209,
Sus scrofa	ENSSSCG00000012783	1 retrocopy	retro_sscr_662,
Tursiops truncatus	ENSTTRG00000011728	1 retrocopy	retro_ttru_848,