RetrogeneDB ID: retro_cjac_1376

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:10659570..10660110(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENOPH1
• Ensembl ID: ENSCJAG00000015251
• Aliases: None
• Description: enolase-phosphatase 1 [Source:HGNC Symbol;Acc:24599]

Sequence

>retro_cjac_1376
GGGAACGGAGCCGATGCTCTGCAACAGATGACCCAGGCTGTGGTAGACAATGTGTGCTGGCAGATGTCCCTGGATGGAAA
GACCACCATGTTCAAACAGCTGCAGGGCCGCATGTGAAGGGCAGCATTCACAGCATGGCTCATGAAAGCAGAGTTATTTG
AGAATGTGTTTCCAGCAGTCAGGAAGTGGAGAGAGGCTGGACTGAAGGAGTGCATCTATTCCTCAGGGAGTGTAGAGGCA
CGGAAATTGTGATTCCGACAGTCTGCAAAGGGATTCTTGAGCTTGTTGATGGTCACTTTGATACAAAGATTGGACATAAA
GTAGAGAGTGAAAGTTATCAGAGGATTGCAGACAGCATCAGGTGCCCAACCAACAACATTTGTTTCTGATAGATGTTACT
TGAGAGGCAAGTGCTGCTGAGGAAGCAGATATGCAGGTAGAGGTGGTGGTGAGACCTGGAACCACAGGATTAATGGATGA
TTAGAAGACTTACTAAGCTTCATCACATCCTTCAGCAAACTGTCCCTGCCCTCCTCAACC

Alignment

ORF - retro_cjac_1376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.51 %
• Parental protein coverage: 69.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSGMDDLQQMIQAVVDNVCWQMSLDRKTTALKQLQGHMWRTAFTAGLMKAEFFADVVPAVRKWREAGMKV
          G.G.D.LQQM.QAVVDNVCWQMSLD.KTT..KQLQG.M.R.AFTA.LMKAE.F..V.PAVRKWREAG.K.
Retrocopy GNGADALQQMTQAVVDNVCWQMSLDGKTTMFKQLQGRM*RAAFTAWLMKAELFENVFPAVRKWREAGLKE

Parental  YVYSSGSVEAQKLLFGHSTEGDILEL-VDGHFDTKIGRKVESESYRKIADSIGCSTNNI-LFLTDVTREA
          ..YSSGSVEA.KL.F..S..G..L.L.VDGHFDTKIG.KVESESY..IADSI.C.TNNI.LFL.DVT.EA
Retrocopy CIYSSGSVEARKL*FRQSAKG-FLSL<VDGHFDTKIGHKVESESYQRIADSIRCPTNNI<LFLIDVT*EA

Parental  SAAEEADVHVAVVVRPGNAGLTDDEKTY-YSLITSFSELYLPSST
          SAAEEAD..V.VVVRPG..GL.DD.KTY..S.ITSFS.L.LPSST
Retrocopy SAAEEADMQVEVVVRPGTTGLMDD*KTY<LSFITSFSKLSLPSST

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	10.38 RPM
SRP051959_heart	0.14 RPM	13.23 RPM
SRP051959_kidney	0.02 RPM	20.17 RPM
SRP051959_liver	0.00 RPM	9.86 RPM
SRP051959_lung	0.00 RPM	14.38 RPM
SRP051959_lymph_node	0.00 RPM	16.05 RPM
SRP051959_skeletal_muscle	0.22 RPM	7.25 RPM
SRP051959_spleen	0.00 RPM	17.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1376 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1376 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1376 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005140	2 retrocopies	retro_amel_1186, retro_amel_930,
Choloepus hoffmanni	ENSCHOG00000003283	4 retrocopies	retro_chof_2150, retro_chof_470, retro_chof_486, retro_chof_596,
Callithrix jacchus	ENSCJAG00000015251	2 retrocopies	retro_cjac_1376 , retro_cjac_2375,
Equus caballus	ENSECAG00000019612	1 retrocopy	retro_ecab_164,
Erinaceus europaeus	ENSEEUG00000004274	1 retrocopy	retro_eeur_563,
Homo sapiens	ENSG00000145293	1 retrocopy	retro_hsap_2900,
Gorilla gorilla	ENSGGOG00000003719	1 retrocopy	retro_ggor_2010,
Loxodonta africana	ENSLAFG00000008619	1 retrocopy	retro_lafr_1158,
Macropus eugenii	ENSMEUG00000011458	1 retrocopy	retro_meug_1125,
Myotis lucifugus	ENSMLUG00000014460	1 retrocopy	retro_mluc_2504,
Otolemur garnettii	ENSOGAG00000002502	1 retrocopy	retro_ogar_1549,
Pongo abelii	ENSPPYG00000014887	1 retrocopy	retro_pabe_2399,
Pan troglodytes	ENSPTRG00000016218	1 retrocopy	retro_ptro_1960,
Tursiops truncatus	ENSTTRG00000001800	1 retrocopy	retro_ttru_1231,