RetrogeneDB ID: retro_cjac_2798

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:31304522..31305138(-)
• Located in intron of: ENSCJAG00000010743

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMZ2
• Ensembl ID: ENSCJAG00000000254
• Aliases: None
• Description: archaelysin family metallopeptidase 2 [Source:HGNC Symbol;Acc:28041]

Sequence

>retro_cjac_2798
TCTGTAAAGATGCTAAAGCCAGTTCTCATTCTAAAGAACACAGCAAGCATATCCCACTATGAGAGCTCAGATACGGGGGA
AGACTTCTCTGAAAGCAAGCTTCCAACTAGAGTGCATTTTGGACCCATTCATTTGCATTTTCAGTGAGCTTGGATCACCT
TCCACAGGGAGGCCTCTGAAGACTGATCAGTTTTCAAAGATCCTTACAGGAGAAATGCCCCAGAGAAATGCAGTATTTCT
ATATAGTCCATTGGAATATATTGGCTCTCTAGGAAACGCCAGAATTATTAGTGTAGAATATATTCAATGGCTCATGAGCT
ACTGTGAAGCATTATTTTGTGGCTTGACAGTACAACTCCCAGAACCAGCTCCTATTTCTGCAATGAGGTGTTCTTTCAGA
CTCACTGACAACGCATAAAACCTGCAAATTCATGTCGGCTCATTCTAAAGTAAAAAAAACAAAAAGGAAACCTAAAGACA
CATTCTATATTGCAGGGATAACAGTGACTGATTTTCACCGGAGAGACACCTAGAATTTTGTGTTTGGACAGGCTTCTTTG
ACAGATGGTGTGGGGAATTCAGCTTTGCCAGGTACAGCAGTGATTTTTATAGTTTG

Alignment

ORF - retro_cjac_2798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.03 %
• Parental protein coverage: 57.22 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SQQTLKTALISKNPVLVSQYENLDAGEQRLMNEAFQPASDLFGPITLHSQSDWITSHPEAPQDFEQFFSD
          S...LK..LI.KN....S.YE..D.GE.....E...P....FGPI.LH.Q..WIT.H.EA..D....F.D
Retrocopy SVKMLKPVLILKNTASISHYESSDTGED--FSESKLPTRVHFGPIHLHFQ*AWITFHREASED*S-VFKD

Parental  PYR-KIPSPDKHSIY--IQSIGSLGNTRIISEEYIKWLQGYCKAYFYGLRVKLLEPVPVSATKCSFRVNE
          PYR...P.......Y.....IGSLGN.RIIS.EYI.WL..YC.A.F.GL.V.L.EP.P.SA..CSFR...
Retrocopy PYR>EMPQRNAVFLYSPLEYIGSLGNARIISVEYIQWLMSYCEALFCGLTVQLPEPAPISAMRCSFRLTD

Parental  NTQNLQIHAGDILKFLKKK-KPEDAFCIVGITMIDLYPRDSWNFVFGQASLTDGV-GIFSFARYGSDFYS
          N..NLQIH.G.......KK.KP.D.F.I.GIT..D...RD..NFVFGQASLTDGV.G.FSFARY.SDFYS
Retrocopy NA*NLQIHVGSF*SKKNKK>KPKDTFYIAGITVTDFHRRDT*NFVFGQASLTDGV<GEFSFARYSSDFYS

Parental  L
          L
Retrocopy L

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	2.40 RPM
SRP051959_heart	0.00 RPM	6.44 RPM
SRP051959_kidney	0.00 RPM	7.03 RPM
SRP051959_liver	0.00 RPM	4.79 RPM
SRP051959_lung	0.00 RPM	5.51 RPM
SRP051959_lymph_node	0.00 RPM	5.71 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.96 RPM
SRP051959_spleen	0.00 RPM	6.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2798 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2798 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2798 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009345	1 retrocopy	retro_btau_429,
Choloepus hoffmanni	ENSCHOG00000000493	1 retrocopy	retro_chof_2462,
Callithrix jacchus	ENSCJAG00000000254	1 retrocopy	retro_cjac_2798 ,
Cavia porcellus	ENSCPOG00000013061	1 retrocopy	retro_cpor_1226,
Equus caballus	ENSECAG00000011450	2 retrocopies	retro_ecab_440, retro_ecab_864,
Felis catus	ENSFCAG00000019195	1 retrocopy	retro_fcat_760,
Myotis lucifugus	ENSMLUG00000006771	2 retrocopies	retro_mluc_1540, retro_mluc_2056,
Mustela putorius furo	ENSMPUG00000014570	1 retrocopy	retro_mputfur_1224,
Pteropus vampyrus	ENSPVAG00000017239	2 retrocopies	retro_pvam_1453, retro_pvam_989,