RetrogeneDB ID: retro_cjac_3907

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286226.1:30483..31238(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001992
• Aliases: None
• Description: None

Sequence

>retro_cjac_3907
AGATATCAGCGGGACATGATCAAGAAGAGAGCCCTGATTGGCTTTGGCTTGACGTCATATAAACATTGACATTCTGGACT
AGTGAATGTGCCTGAGGAACCTATTGAAGAGGAGGGAGAGGAGGAGGTGGAAGAGGAGGAAGAAGACCAGGACATGGATG
CAGATGATGGAGTGGTGGTAGAGTACCACGAAGAGTTCTGGGAACAGAGCGTATCTAGACCATCCAGTGCCAGCAACTCA
GACTCAGATGAAATGGACTATAATCTAGAACTGAAGATGACTTCCACTGCTTCACCAGAGAAAAGCATGAAAATGACTAT
GTATGCTGATTAAGTGGAATCTCAGTTGAATAACATTAGGAACTCCATGAGGGTACATAGCGTATCTTCAAGTAATATCA
AAAACCAAATTGGTAAGAAACCACCACCTGAGAAATTTGCAGATGTCTGACATCTATTAGATGAAAAACACCAGCACTGG
TGTCCACAGCCACCAGTCAGCAACACTAAATCAGATAAATGCCAGCAGTTAGGAAAAAGACCATATTCTCCAGAACAGGC
TTTTAGTTGTAACCCAGTGGTTCGGAGAGAGCCCTCTTCTGATGTTCATAGGAGGCTAGGTATTACCAGGCAAGATATTA
AAGGCCTCTACTCTGAAACTTGGGAGAAGAAATCAGGTAATTTTGGACTCATTTTGGATCTGCACCCAAGACCAAAGAAA
AGAATACGAAGAACAGGGATCACAAGGCACCAGGC

Alignment

ORF - retro_cjac_3907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.03 %
• Parental protein coverage: 51.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RIQRDVIKKRALIGDDVGLTSYKHRHSGLVNVPEEPIEEEEEEEEEEEEEDQDMDADDRVVVEYHEELPA
          R.QRD.IKKRALIG...GLTSYKH.HSGLVNVPEEPI..............QDMDADD.VVVEYHEE...
Retrocopy RYQRDMIKKRALIG--FGLTSYKH*HSGLVNVPEEPIXXXXXXXXXXXXXXQDMDADDGVVVEYHEEF--

Parental  LKQSKDRSTSRRSSASSSDSDEMDYDLELKMISTPSPKKSMKMTMYADEVESQLKNIRNSMRADSVSSSN
          ..QS..R..S...S.S....DEMDY.LELKM.ST.SP.KSMKMTMYAD.VESQL.NIRNSMR..SVSSSN
Retrocopy WEQSVSRPSSASNSDS----DEMDYNLELKMTSTASPEKSMKMTMYAD*VESQLNNIRNSMRVHSVSSSN

Parental  IKNRIGNKPPPEKFADVRHLLDEKRQHSRPRPPVSNTKSDIRQRLGKRPYSPEKAFSSNAVVRREPSSDV
          IKN.IG.KPPPEKFADV.HLLDEK.QH..P.PPVSNTKSD..Q.LGKRPYSPE.AFS.N.VVRREPSSDV
Retrocopy IKNQIGKKPPPEKFADV*HLLDEKHQHWCPQPPVSNTKSDKCQQLGKRPYSPEQAFSCNPVVRREPSSDV

Parental  HSRLGVPRQDIKGLYADTREKKSGN-LWTRLGSAPKTKEKSTKKGDHRAPG
          H.RLG..RQDIKGLY..T.EKKSGN..WT..GSAPKTKEK.TK..DH.APG
Retrocopy HRRLGITRQDIKGLYSETWEKKSGN<FWTHFGSAPKTKEKNTKNRDHKAPG

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	7.94 RPM
SRP051959_heart	0.00 RPM	7.96 RPM
SRP051959_kidney	0.00 RPM	9.43 RPM
SRP051959_liver	0.00 RPM	5.96 RPM
SRP051959_lung	0.00 RPM	12.25 RPM
SRP051959_lymph_node	0.00 RPM	13.90 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.08 RPM
SRP051959_spleen	0.00 RPM	12.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3907 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3907 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3907 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001992	1 retrocopy	retro_cjac_3907 ,