RetrogeneDB ID: retro_cjac_2262

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:112241243..112242017(-)
• 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_2262
TCTTTTCGGGCTTGCTTCAAGAAGTATCTTCCGCATCCATATAGAAACTGGCAACATCTGGACCCATCTGCTTGGTTTGT
GCTGTTTCTCTTTTAGGAATCTGACCATGCTCAGACCAAATATGTACTTCGTGGCCCCTCTACAGGAGAAGGTGTTTTTT
GGGATGTTCTTCTTGGGTGTAGTGCTCTGCCTCAGTTTCTCCTGCCTCTTTCATTCCATTTATTCTCATTAGAGAAAGTG
TCTCAGACTTTTTCCAAACTGAACTATTCAGGGATTGCTCTTCTAATTATCAGGAGCTTTGTCCCCTGGCTCTATTATTC
CTTCTACTGCTCCCCATAGCCACGGCTCATCTACTTCTCCATCATCTGCATCCTGGGCATTTCTGCCATCATTGTGGCAC
AGTGGGACCAGTTTGCCACTCCTAAGCACCGGCTGACAAGAGCAGGGGTGTTCCTGGGACTTGGCTTGAGTGGTGTCGTG
CCCACCATACACTTTACTATTGCTGAGGGCTTTGTCAAGGCCACCACACTGGGCCAGATGGGCTGGTTCTTCCTCATGGC
TGTGATGTACATCACTGGAGCTGGCCTTTATGCTACTCGAATTCCTGAGCACTTCTTTCCTGGAAAATTAGACATATGGT
TCCAGTCTCATCAGATTTTCCATGTCCTGGTGGTGGCAGCAGCCACCAGAAGTTAGGTCCACTTCTATGGGGTCTCCAAT
CTTCAGGAATTCCATTATGGCCTAGAAGGTGGCTGTACTGATGACACCCTTCTC

Alignment

ORF - retro_cjac_2262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.12 %
• Parental protein coverage: 68.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SFRACFK-SIFRIHTETGNIWTHLLG-FVLFLF-LGI-LTMLRPNMYFMAPLQEKVVFGMFFLGAVLCLS
          SFRACFK.SIFRIH.ETGNIWTHLLG.FVLFLF.LGI.LTMLRPNMYF.APLQEKV.FGMFFLG.VLCLS
Retrocopy SFRACFK>SIFRIHIETGNIWTHLLG<FVLFLF<LGI<LTMLRPNMYFVAPLQEKVFFGMFFLGVVLCLS

Parental  FSWLFHTVYCH-SEKVSRTFSKLDYSGIALLIMGSFVPWLYYSFYCSPQPRLIYLSIVCVLGISAIIVAQ
          FS.LFH..Y.H..EKVS.TFSKL.YSGIALLI..SFVPWLYYSFYCSP.PRLIY.SI.C.LGISAIIVAQ
Retrocopy FSCLFHSIYSH<LEKVSQTFSKLNYSGIALLIIRSFVPWLYYSFYCSP*PRLIYFSIICILGISAIIVAQ

Parental  WDRFATPKHRQTRAGVFLGLGLSGVVPTMHFTIAEGFVKATTVGQMGWFFLMAVMYITGAGLYAARIPER
          WD.FATPKHR.TRAGVFLGLGLSGVVPT.HFTIAEGFVKATT.GQMGWFFLMAVMYITGAGLYA.RIPE.
Retrocopy WDQFATPKHRLTRAGVFLGLGLSGVVPTIHFTIAEGFVKATTLGQMGWFFLMAVMYITGAGLYATRIPEH

Parental  FFPGKFDIWFQSHQIFHVLVVAAAF---VHFYGVSNLQEFRYGLEGGCTDDTLL
          FFPGK.DIWFQSHQIFHVLVVAAA....VHFYGVSNLQEF.YGLEGGCTDDTLL
Retrocopy FFPGKLDIWFQSHQIFHVLVVAAATRS*VHFYGVSNLQEFHYGLEGGCTDDTLL

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	20.39 RPM
SRP051959_heart	0.02 RPM	28.87 RPM
SRP051959_kidney	0.04 RPM	34.37 RPM
SRP051959_liver	0.11 RPM	34.18 RPM
SRP051959_lung	0.00 RPM	30.99 RPM
SRP051959_lymph_node	0.05 RPM	19.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	31.47 RPM
SRP051959_spleen	0.02 RPM	31.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2262 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2262 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,