RetrogeneDB ID: retro_cjac_3873

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285540.1:11072..12323(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1M1
• Ensembl ID: ENSCJAG00000014070
• Aliases: None
• Description: None

Sequence

>retro_cjac_3873
ATGTCTGCCTCAGCTGTCTTTATTCTCGACATCAAGGGCAAGTCTCTGATGAGCCACAACTACAAAGGCGATTAGCCCTT
GAGTAAGATGGAGCACTTCATGCCTCTGCTGGTACAGTGGGAGGATGAGGGTGCCCTGACTCTGCTTCTGAGCTATGGTG
AGGCCCACTTCCTATGGATCAAACAAAGCAGCCTCTACTTGGTGGCCACCACATTGAAGAATGCCAATGCCACCTTTTTT
TATAAGACAATACAGTTGTTCTGTGAATACTTCAAGGAACTAGAGGAGGAGAGCATCTGGGACAGCTTTGTCATCATCTA
CAAATTGCTGAATAAGCTGATGGACTTTGGCTTCCTGCAGAGCACCGACAGCAAGATCCTGCAAGAGTACATCAGTCAGC
AGAGCAACAAGCTGGAGACAGGCAAGAGGGTGCCACCCACTGTCACCAACGCTGTGTGGTGGCACTCTGAGGGTATCAAG
TATAAGAACGAGGTCTTCATCGATTTCATAGAGTTGTCAACCTGCTGGTCAATGCCAATGGCAACATCCTGCTGAGTGAG
ATTGTGGGTACCATCAAGCTCAAGGTGTTTCTGTTGGGAATGCCAGAGTCGTGGCTGAGCCTCAATCACTGCGTGCTCTT
CGAGCTCACTGGCCTTTCAGGGAGCAAGAACAAATCAATAAAGCTAAAGGATGTAAAATTCCACCAGCACATGTGGCTCT
CATGCTTTGGCAATGACCGCACCAACTCCTTCATCCCATCTGATGGTGACTTTAAGCTCATGTCCTACCTCCTCAGCACC
CAGGTGAAGCTACTGATCTGGATTGGGTCTATCATTGAGAAGTTCTCCCAGAGCCACGTGGAGATCATGGTCAAGGCCAA
GGGGCAGTTAAGAAACAGCCAGTGGCCACCAGTGTGGATATACCTGTGACCATGCCCAGCAATGCCAACTCCCCCAGATT
CAAGACCAGTGTGGGCAGCACCAAGTATGTGCCAGAGAAAAATGTCGTAATTTGGAGTATTAAGTCTTTCCTGGGGGCAA
GGAGTACTCGCTGCGAGCCCACTTTGGTCTCCCCAGCATGGAGAAGGAGGAGCTGGAGGGCTGGCCCCCAATCGGGGTCA
AGTTTGAGATCCCCTACTTCACCATCTCTGGGATCCAGGTCCGATACATTAAGATTATTGAGAAAAGTGGTTACCAGGCC
CTGCCCTGCGTTTGCTACATCACCCAGAGTGGGGATTACCAACTTTGTACC

Alignment

ORF - retro_cjac_3873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.7 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVAT
          MSASAV..LD.KGK.L...NY.GD...S..EHFMP.L...E.EG.L...L..G...F.WIK...LYLVAT
Retrocopy MSASAVFILDIKGKSLMSHNYKGD*PLSKMEHFMPLLVQWEDEGALTLLLSYGEAHFLWIKQSSLYLVAT

Parental  SKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQEYITQEGH
          ..KNA..........K..Q.F.EYFKELEEESI.D.FVIIY.LL..LMDFG..Q.TDSKILQEYI.Q...
Retrocopy TLKNANATFFY----KTIQLFCEYFKELEEESIWDSFVIIYKLLNKLMDFGFLQSTDSKILQEYISQQSN

Parental  KLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIE-SVNLLVSANGN-ACSEIVGSIKMRVFLSGMPE
          KLETG..R.P.TVTNAV.W.SEGIKY.KNEVF.D.IE..VNLLV.ANGN...SEIVG.IK..VFL.GMPE
Retrocopy KLETG-KRVPPTVTNAVWWHSEGIKY-KNEVFIDFIE<VVNLLVNANGNILLSEIVGTIKLKVFLLGMPE

Parental  LRLGLNDKVLFDNTG--RGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLI
          ..L.LN..VLF..TG....K.KS..L.DVKFHQ...LS.F.NDRT.SFIP.DG.F.LMSY.L.T.VK.LI
Retrocopy SWLSLNHCVLFELTGLSGSKNKSIKLKDVKFHQHMWLSCFGNDRTNSFIPSDGDFKLMSYLLSTQVKLLI

Parental  WIESVIEKHSHSRIEYMIKAKSQF-KRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSIK
          WI.S.IEK.S.S..E.M.KAK.Q..K....A..V.I....P..A.SP.FKT.VGS.K.VPE.....WSIK
Retrocopy WIGSIIEKFSQSHVEIMVKAKGQL<KKQPVATSVDIPVTMPSNANSPRFKTSVGSTKYVPEKNVVIWSIK

Parental  S-FPGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQN
          S.FPGGKEY..RAHFGLPS.E.E..EG.PPI.VKFEIPYFT.SGIQVRY.KIIEKSGYQALP.V.YITQ.
Retrocopy S<FPGGKEYSLRAHFGLPSMEKEELEGWPPIGVKFEIPYFTISGIQVRYIKIIEKSGYQALPCVCYITQS

Parental  GDYQLRT
          GDYQL.T
Retrocopy GDYQLCT

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	6.66 RPM
SRP051959_heart	0.00 RPM	10.80 RPM
SRP051959_kidney	0.00 RPM	13.67 RPM
SRP051959_liver	0.00 RPM	14.95 RPM
SRP051959_lung	0.00 RPM	10.87 RPM
SRP051959_lymph_node	0.00 RPM	13.95 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.58 RPM
SRP051959_spleen	0.00 RPM	12.98 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3873 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3873 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012998	1 retrocopy	retro_cjac_3340,
Callithrix jacchus	ENSCJAG00000014070	3 retrocopies	retro_cjac_1985, retro_cjac_2135, retro_cjac_3873 ,