RetrogeneDB ID: retro_cjac_554

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:77089062..77090429(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFN1
• Ensembl ID: ENSCJAG00000013155
• Aliases: None
• Description: None

Sequence

>retro_cjac_554
AACCAATTGCTTCCTGTTTAAAGAACCAGTGGACATAAAACCTATCTTATGACAAAAGGATAAGATAAAAAGAGTGTGAA
GACAGTTCATCAGCTGTCCTATGCCCTTCATATGGACAAAGACTTGGAAGCTCGCTGTCTTATCCATGTGTTTTGGCCAA
AGACAAAGTGTGTCCTCTTGAGAGGTGAGCTGGTTTTAGTAGACAGTCCAGGCACAGATGTCACAACAGAGCTGGACACC
TGAATTGATGAGCATTGCTTAGATGTTCATGTCATTTTGGTTGTAAACTCTGAATCGACACTAGCAAACACAGAAAAACA
TTTCTTCACAAGGCAAATGAGCAGTTTTCCAAGCCTAATAATTTAATTCTGAATAATTACTGGGATGTGTCTTCATCAGA
GCCAGAATATATGGAAGATGCATGCACACAGCACATAGAAAGATGCTTGCATTTCTTTGTGGAGAAGCTTCAAGTTGTAG
ATCCTTTAGAAGCACAGAATGACATATTCTTTATTTCAGCAAAGCAAGTTCTTAGTGCTAGATGGTACAAACCACAGGAG
ATGCCAGAAGGCAGTGAAGTACTTGCTAAAGGATTTCAAGAAAGATAATAGGAGTTTCAGAATTTTAAACAAATCTTTGA
GGAATATATATCACAATCAGCAGTGAAAACAAGGTTCAAACAGCATATAATCAGAGCTAAGTCAATACAAGATATCGCAA
AAAACACAATGGATTCAATAAACGTGGCAGCAACAGAGAAGAGCTTATTCAAAGAAAGAGCGGGAAGAACAAACTGATAG
ACTGGACTTTATCCAAAACCAGTTGAACCTTTTAACACTAGATGTTAAGAAAAAAATCAGAGAGGTTACCAAGGAAGTGG
CAAACAAGGTTTCATGTGCAAAGACAGATGAAATTTGTTGACTGTTTGCTTTGGTTGATGAATTTTGCTCAGAGTTTCAT
TCTACTCCAAGTGTAATGAAAGAATACAAAGATGATTTAAATAGGCACTTAGAAGACAGTATCAGAAGAAATATGGCTGA
TTGATGCACCAGTGAAGACAATGACTCAATGTCTAACCCCAGCAAGAAGTTATTAAAAATTTAAAACCATTACTTCCAGC
TGATATACAGACTAAACTGCATACACTGACCCCTTGCAAGAAATCTGATCTCAGTTATGACCTATATCGCCACAAGTTAT
GGCCAGATTTTCAAGAGGATACTGTATTCCATTTTTCCCTGAGCTGGTCTTCACTTGTGGATTGATTCCTGGGCCCTACA
AATACTCAGAGGGTGCGTTCAGGATTGTCAAAGCCTATCTTTCCCTAGCTCTTTAGCCTCTACTCCCACTGCTCCTACCA
ACCCAGT

Alignment

ORF - retro_cjac_554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.75 %
• Parental protein coverage: 59.69 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NCFLSVEGTDGDKAYLMTEGSDEKKSVKTVNQLAHALHMDKDLKAGCLVHVFWPKAKCALLRDDLVLVDS
          N..L.V..T.G.K.YLMT.G.D.KKSVKTV.QL..ALHMDKDL.A.CL.HVFWPK.KC.LLR..LVLVDS
Retrocopy NQLLPV*RTSGHKTYLMTKG*D-KKSVKTVHQLSYALHMDKDLEARCLIHVFWPKTKCVLLRGELVLVDS

Parental  PGTDVTTELDSWIDKFCLDADVFVLVANSESTLMNTEKHFF-HKVNERLSKPNIFILNNRWDASASEPEY
          PGTDVTTELD..ID..CLD..V..LV.NSESTL.NTEKHFF.HK.NE..SKPN..ILNN.WD.S.SEPEY
Retrocopy PGTDVTTELDT*IDEHCLDVHV-ILVVNSESTLANTEKHFF<HKANEQFSKPNNLILNNYWDVSSSEPEY

Parental  MEDVRRQHMERCLHFLVEELKVVNALEAQNRIFFVSAKEVLSARKQKAQGMPEGGGALAEGFQARLQEFQ
          MED...QH.ERCLHF.VE.L.VV..LEAQN.IFF.SAK.VLSAR..K.Q.MPEG...LA.GFQ.R..EFQ
Retrocopy MEDACTQHIERCLHFFVEKLQVVDPLEAQNDIFFISAKQVLSARWYKPQEMPEGSEVLAKGFQER**EFQ

Parental  NFEQIFEECISQSAVKTKFEQHTIRAKQILATVKNIMDSINVAAEEKRAY-SVEEREDQIDRLDFIRNQM
          NF.QIFEE.ISQSAVKT.F.QH.IRAK.I....KN.MDSINVAA.EK......E..E.Q.DRLDFI.NQ.
Retrocopy NFKQIFEEYISQSAVKTRFKQHIIRAKSIQDIAKNTMDSINVAATEKSLF>KKEREE-QTDRLDFIQNQL

Parental  NLLTLEVKRKIKEVTEEVANKVSCAMTDEICRLSVLVDEFCSEFHPTPDVLKIYKSELNKHIEDRMGRKL
          NLLTL.VK.KI.EVT.EVANKVSCA.TDEIC.L..LVDEFCSEFH.TP.V.K.YK..LN.H.ED...R..
Retrocopy NLLTLDVKKKIREVTKEVANKVSCAKTDEIC*LFALVDEFCSEFHSTPSVMKEYKDDLNRHLEDSIRRNM

Parental  ADRCTDEVNA-LVLQSQEEIIENLKPLLPAGIQDKLHTLISCKKFDLSYNLNYHKLCSDFQEDIVFHFSL
          AD.CT.E.N..L....Q.E.I.NLKPLLPA.IQ.KLHTL..CKK.DLSY.L..HKL..DFQED.VFHFSL
Retrocopy AD*CTSEDND<LNV*PQQEVIKNLKPLLPADIQTKLHTLTPCKKSDLSYDLYRHKLWPDFQEDTVFHFSL

Parental  GWSSLVHRFLGPRNAQRVLLGLSEPIFQLPRSLASTPTAPPS
          .WSSLV..FLGP.N.QRV..GLS.PIF....SL.S.....PS
Retrocopy SWSSLVD*FLGPTNTQRVRSGLSKPIFP*LFSLYSHCSYQPS

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	27.29 RPM
SRP051959_heart	0.00 RPM	63.07 RPM
SRP051959_kidney	0.00 RPM	34.63 RPM
SRP051959_liver	0.00 RPM	28.98 RPM
SRP051959_lung	0.00 RPM	31.97 RPM
SRP051959_lymph_node	0.00 RPM	30.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	30.77 RPM
SRP051959_spleen	0.00 RPM	33.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_554 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_554 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013155	1 retrocopy	retro_cjac_554 ,
Nomascus leucogenys	ENSNLEG00000005745	1 retrocopy	retro_nleu_1240,
Pongo abelii	ENSPPYG00000014318	1 retrocopy	retro_pabe_3682,