RetrogeneDB ID: retro_cjac_740

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:120238876..120239702(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADIPOR1
• Ensembl ID: ENSCJAG00000006268
• Aliases: None
• Description: adiponectin receptor 1 [Source:HGNC Symbol;Acc:24040]

Sequence

>retro_cjac_740
CCTGACTGGCTGAAGGACAATGACTGTCTGCTATATGGCCATAGCCAACCCATGCCCTCCTTCTGGTCTTGCTTCAAGAG
CATCTTCTACATCCATACAGAAACCAGCAACATCTGGACCCATCTGCTTCACTTCGTGCTGTTTCTCTTTTTGGGAATCT
TGACCATGCTCAGACCAAATATGTACTTCATGGATCCTCTACAAGAGAAAGTGGTTGAGGGATATTCTTTCTGGGTGCAG
TGCTCTGACTCAGCTTCTCCTGGCTCATCCACACCATCTACAGTCATTCAAAGAAAGTTTCTCAGACTTTTCCAAACTGG
ACTATTCAGGGATTGCTCCACTGATTATAAGGAGCTTCTTTCCCTGGCTCTGTTCCTCCTCCTACTGCTCCCCACAGCCA
CAGCCCATCTACCTCTCCATCGTCTGTGTCCTGGGCATCTCTGCCATCCTTGTGGCACAGTGGGACTTGTTTGCCACTTC
TAAGCACCCACAGTAAGGGCAGGGGTGTTGCTGGGACTTGGCTTGAGTGGTGTTGTGCTCACCATGCACTTTACTATCGC
TGAGTGAGGACTTTGCCAAGGTCACCACAGTGGGCCAGATGGGCTGGTTCTTCCTTGTGACTGTCACGTACATCACCAGA
GCTGGCCTTTATGCCTCTTGGATTCCTGAACACTTCTTTCCTGGAGAATTTGATGTATGGTTCCAGTCTCAGCCAATTTC
CCATGTCCTCATGGTGACAGTGGCCTTTGTCCATTTCTGTGGGGTCTCCAACCTTCAGGAATTCTGTTACAGCCGAGAAG
GTGGCTGCACTGATGACTTGGTTCTG

Alignment

ORF - retro_cjac_740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.64 %
• Parental protein coverage: 74.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PGRLKDNDYLLHGHRPPMPSFRACFKSIFRIHTETGNIWTHLLGFVLFLFLGILTMLRPNMYFMAPLQEK
          P..LKDND.LL.GH..PMPSF..CFKSIF.IHTET.NIWTHLL.FVLFLFLGILTMLRPNMYFM.PLQEK
Retrocopy PDWLKDNDCLLYGHSQPMPSFWSCFKSIFYIHTETSNIWTHLLHFVLFLFLGILTMLRPNMYFMDPLQEK

Parental  VVF-GMFFLGAVLCLSFSWLFHTVYCHSEKVSRT-FSKLDYSGIALLIMGSFVPWLYYSFYCSPQPRLIY
          VV..G.FFLGAVL.LSFSWL.HT.Y.HS.KVS.T.FSKLDYSGIA.LI..SF.PWL..S.YCSPQP..IY
Retrocopy VVE<GIFFLGAVL*LSFSWLIHTIYSHSKKVSQT<FSKLDYSGIAPLIIRSFFPWLCSSSYCSPQPQPIY

Parental  LSIVCVLGISAIIVAQWDRFATPKHRQ-TRAGVFLGLGLSGVVPTMHFTIAE-GFVKATTVGQMG-WFFL
          LSIVCVLGISAI.VAQWD.FAT.KH.Q..RAGV.LGLGLSGVV.TMHFTIAE.G.......G..G.WFFL
Retrocopy LSIVCVLGISAILVAQWDLFATSKHPQ<VRAGVLLGLGLSGVVLTMHFTIAE*GLCQGHHSGPDG>WFFL

Parental  MAVMYITGAGLYAARIPERFFPGKFDIWFQSHQIFHVLVVAAAFVHFYGVSNLQEFRYGLEGGCTDDTLL
          ..V.YIT.AGLYA..IPE.FFPG.FD.WFQS..I.HVL.V..AFVHF.GVSNLQEF.Y..EGGCTDD..L
Retrocopy VTVTYITRAGLYASWIPEHFFPGEFDVWFQSQPISHVLMVTVAFVHFCGVSNLQEFCYSREGGCTDDLVL

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	20.39 RPM
SRP051959_heart	0.00 RPM	28.87 RPM
SRP051959_kidney	0.00 RPM	34.37 RPM
SRP051959_liver	2.32 RPM	34.18 RPM
SRP051959_lung	0.00 RPM	30.99 RPM
SRP051959_lymph_node	0.00 RPM	19.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	31.47 RPM
SRP051959_spleen	0.00 RPM	31.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_740 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_740 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012199	1 retrocopy	retro_amel_1853,
Choloepus hoffmanni	ENSCHOG00000006450	8 retrocopies	retro_chof_1127, retro_chof_1222, retro_chof_1917, retro_chof_2218, retro_chof_2380, retro_chof_471, retro_chof_749, retro_chof_995,
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,
Cavia porcellus	ENSCPOG00000000482	1 retrocopy	retro_cpor_470,
Dipodomys ordii	ENSDORG00000006876	1 retrocopy	retro_dord_19,
Felis catus	ENSFCAG00000013565	1 retrocopy	retro_fcat_1514,
Loxodonta africana	ENSLAFG00000003520	1 retrocopy	retro_lafr_277,
Macropus eugenii	ENSMEUG00000015439	1 retrocopy	retro_meug_516,
Microcebus murinus	ENSMICG00000007942	3 retrocopies	retro_mmur_1199, retro_mmur_184, retro_mmur_764,
Myotis lucifugus	ENSMLUG00000016102	2 retrocopies	retro_mluc_1275, retro_mluc_200,
Macaca mulatta	ENSMMUG00000007046	1 retrocopy	retro_mmul_1322,
Mustela putorius furo	ENSMPUG00000011215	1 retrocopy	retro_mputfur_550,
Otolemur garnettii	ENSOGAG00000033821	4 retrocopies	retro_ogar_1558, retro_ogar_1624, retro_ogar_2838, retro_ogar_783,
Ochotona princeps	ENSOPRG00000004528	3 retrocopies	retro_opri_101, retro_opri_1050, retro_opri_392,
Pongo abelii	ENSPPYG00000000342	1 retrocopy	retro_pabe_1072,
Sorex araneus	ENSSARG00000007680	1 retrocopy	retro_sara_25,
Ictidomys tridecemlineatus	ENSSTOG00000015459	3 retrocopies	retro_itri_215, retro_itri_257, retro_itri_512,
Tupaia belangeri	ENSTBEG00000015149	2 retrocopies	retro_tbel_1501, retro_tbel_1804,
Tarsius syrichta	ENSTSYG00000001491	1 retrocopy	retro_tsyr_125,
Tursiops truncatus	ENSTTRG00000006381	2 retrocopies	retro_ttru_1055, retro_ttru_863,