RetrogeneDB ID: retro_cjac_504

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:15202180..15203008(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADIPOR2
• Ensembl ID: ENSCJAG00000000683
• Aliases: None
• Description: adiponectin receptor 2 [Source:HGNC Symbol;Acc:24041]

Sequence

>retro_cjac_504
CCCCAGGAAAGGGAGGAGAAGGTGCAGCTACTGAAGCGCTGCACTTCCACCATGCCACGGAGAAGATGGAGGAGTTTGTG
TACAAGGTCTGGGAGGGACGCTGGAGGGTCATTTTATATGATGTGCTCCCTGACTGGCTGAAGGACAAGGCTCCCTGCTA
CATGGCCATAGATCACCCATGCCTTCCTTTTGGGCTTGCTTCAAGAGCATCTTCCACATCCATGCGGAAACAGGCAACAT
CTGGATCCATCTGCTCAGTTTCATGCTGTTTCTCTTTTGGGGATCTTGGCCATGCTCAGCCCAAATATGTACTTCATGGC
CCCTCTATAGGAGAAGGCGGTCTGGGAACGTCCTTTGTGGGTGTAGTGCTCTGCCTCCAAATAGTCGGCTCCTCCTGGCT
ATTCCACACTGTCTATTGTCATTCAGAGAAAGTCTCTCAGACTTTTTCCAAACTGGACTATTCAGCAATTGCTCTACTGA
TTACGGGGAACTTTGTACCGTGGCTCTGCTACTCCTTCCACTGCTCCCCACAGCCACAGCTCATCTTGCTTCTTCTTTGT
CTGTGTCCTGGGCATTTCTGCCATCACAGTAGCACAGTGGGACCAGTTTCTACTCCTAACCACTGGCAGACACAGCAGGA
GCATTCCTGGGACTTGGCTTGAGTGTGATCATGCCCATGATGCATTTTCCTATCAGTGAAGTTCTGTCAGGGCCACAGTC
ATAGTCTGGATAGGTTGGTCCTTCCTCACAGCTGTGATGCACATCACTAGAGCTGGCCTTCATGCTATTTGAATTTCTGA
ATGCTACTTTCATGGAAAATCTGACATG

Alignment

ORF - retro_cjac_504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.49 %
• Parental protein coverage: 71.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  PQEDE-GFMGMSPLLQAHHAMEKMEEFVCKVWEGRWRVIPHDVLPDWLKDN-DFLLHGHRPPMPSFRACF
          PQE.E.G.......L..HHA.EKMEEFV.KVWEGRWRVI..DVLPDWLKD....LLHGHR.PMPSF.ACF
Retrocopy PQERE<GEGAATEALHFHHATEKMEEFVYKVWEGRWRVILYDVLPDWLKDK<GSLLHGHRSPMPSFWACF

Parental  KSIFRIHTETGNIWTHLLGCVFFL-CLGIFYMFRPNISFVAPLQEKVVF-GLFFLGAILCLSF---SWLF
          KSIF.IH.ETGNIW.HLL....FL..LGI..M..PN..F.APL.EK.V..G..F.G..LCL.....SWLF
Retrocopy KSIFHIHAETGNIWIHLLSFMLFL<LLGILAMLSPNMYFMAPL*EKAVW<GTSFVGVVLCLQIVGSSWLF

Parental  HTVYCHSEGVSRIFSKLDYSGIALLIMGSFVPWLYYSFYCNPQPCFIYLIV-ICVLGIAAIIVSQWDMF-
          HTVYCHSE.VS..FSKLDYS.IALLI.G.FVPWL.YSF.C.PQP..I.L....CVLGI.AI.V.QWD.F.
Retrocopy HTVYCHSEKVSQTFSKLDYSAIALLITGNFVPWLCYSFHCSPQPQLILLLL>VCVLGISAITVAQWDQF<

Parental  ATPQYRGVR-AGVFLGLGLSGIIPTLHYVISE-GFLKAATIGQIGWLMLMASLYITGAALYAARIPERFF
          .TP.......AG.FLGLGLS.I.P..H..ISE.....A..I..IGW..L.A...IT.A.L.A..I.E..F
Retrocopy STPNHWQTQ<AGAFLGLGLSVIMPMMHFPISE<SSVRATVIVWIGWSFLTAVMHITRAGLHAI*ISECYF

Parental  PGKCDI
          .GK.D.
Retrocopy HGKSDM

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	15.18 RPM
SRP051959_heart	0.00 RPM	18.43 RPM
SRP051959_kidney	0.00 RPM	19.19 RPM
SRP051959_liver	0.00 RPM	21.86 RPM
SRP051959_lung	0.00 RPM	16.80 RPM
SRP051959_lymph_node	0.00 RPM	12.81 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.75 RPM
SRP051959_spleen	0.00 RPM	14.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_504 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_504 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1072
Macaca mulatta	retro_mmul_1322

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009050	1 retrocopy	retro_btau_320,
Callithrix jacchus	ENSCJAG00000000683	3 retrocopies	retro_cjac_2912, retro_cjac_3290, retro_cjac_504 ,
Callithrix jacchus	ENSCJAG00000006268	3 retrocopies	retro_cjac_2262, retro_cjac_740, retro_cjac_741,
Loxodonta africana	ENSLAFG00000021355	1 retrocopy	retro_lafr_249,
Microcebus murinus	ENSMICG00000005653	1 retrocopy	retro_mmur_818,
Myotis lucifugus	ENSMLUG00000002211	1 retrocopy	retro_mluc_66,