RetrogeneDB ID: retro_cjac_464

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:134237206..134238170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001118
• Aliases: None
• Description: None

Sequence

>retro_cjac_464
AGTAAACATGAGAAGATCATTTTAGACAAAAAGTATCCACAATTGGAGCCCTCCACACTTGCTTGTAAAATAAAGTTGCT
CTCCTTTTGTGAAAGGCAGTGTGTGTTCGTCAATAAAGTTGTGGTACACATGAGATCAATTTTGGCAAATTCCTCAACAA
GCTCTCCTGCTCTAGGATCAAGGATACACCTTGACAAGGTCCAAACCGTAATGGAGTCCATGGGGTCAAAGTTATCTCCT
GGAGCTCAGCAGTTGATGGATATGGTTAGGTTTCAGCAGCAGAGTTGTATTCCCATTAGAGAGCAGCTTCAGTTGGTGTT
GGGCAATACTGTATACAAGCTTGTGATTGGACTAAAATCCTCATCTGCCTTAGGAGCCTTAGACAAGTCATCCTCCACAC
CTTTTCCTTTTAGAACTAGATTGACATCTAGGAACATGACTGAAAACTTAGAAACTTACATTGATAAAAGTACACAGCTA
CCTGGTAAAGAGAATTCTACAAAGTTCGATGAGTGTAACATTATGCCTCAAAACCATTCCCTTCTTGAAAATGTTCTTTA
TAATGCAATATCCTCTTTCTTATAAAAGAAAGCAAGTGACAACTCAAATATACCTAACTCTGAATTGCTACCTTTTTTCT
AGAATTTATGTAATCAAGTTAATCATCTCCATCTGGGAAATAAGACCAAGTGTCAGGAAAACATCACCAAGCATGATGAA
TGCATTCTTAGTGTTAAAATAGAAGAGCAACCTATTTGCTGTACTTGGAAAAGATTCTTTCTAAAAATATGGAACTGATG
GAAAAGAAATTATGGATTACATTTATCAGCAAATATTTGAACTCCAGGTGTACAGTAATAATAAGATTGCTTTGTTAATG
AACTTGCTGTAAAATCCCAACATCCCACCCACTAAAATACCTCTAAGACATGACTCTGGAGAAAGACTTTCAAATGGAGA
AAGA

Alignment

ORF - retro_cjac_464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 72.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGHEKIILYKKYLKLEPSTHACKIKLLSFGERQCVFISKVVVHMRSVLASSSTSSPALGSRIDLHKVQTI
          S.HEKIIL.KKY..LEPST.ACKIKLLSF.ERQCVF..KVVVHMRS.LA.SSTSSPALGSRI.L.KVQT.
Retrocopy SKHEKIILDKKYPQLEPSTLACKIKLLSFCERQCVFVNKVVVHMRSILANSSTSSPALGSRIHLDKVQTV

Parental  MESMGSKLSPGAQQLMDMVRFQQQNCSPIGEQLHSVLANTGYKHMIGLQSSSTLGALDKSSSTPFPFRTG
          MESMGSKLSPGAQQLMDMVRFQQQ.C.PI.EQL..VL.NT.YK..IGL.SSS.LGALDKSSSTPFPFRT.
Retrocopy MESMGSKLSPGAQQLMDMVRFQQQSCIPIREQLQLVLGNTVYKLVIGLKSSSALGALDKSSSTPFPFRTR

Parental  LTSGNVTENLQAYIEKSTQLPGGENSAKLDECKIVPQNHSPPENDLKNAMSCFLPKKASDNSNIPNSELL
          LTS.N.TENL..YI.KSTQLPG.ENS.K.DEC.I.PQNHS..EN.L.NA.S.FL.KKASDNSNIPNSELL
Retrocopy LTSRNMTENLETYIDKSTQLPGKENSTKFDECNIMPQNHSLLENVLYNAISSFL*KKASDNSNIPNSELL

Parental  PFLQNLCSQVNHLRVGNKTECQENITKHG--ILGVGMEEQPL-FSYLEKILSKNMELMEKKL-MDYIDQR
          PF..NLC.QVNHL..GNKT.CQENITKH...IL.V..EEQP....YLEKILSKNMELMEKKL.MDYI.Q.
Retrocopy PFF*NLCNQVNHLHLGNKTKCQENITKHDECILSVKIEEQPI<LLYLEKILSKNMELMEKKL<MDYIYQQ

Parental  IYKLQEHIDDKIALLMDLLQNPNSPPSGMPLRHYDSGERLSNGER
          I..LQ.....KIALLM.LL.NPN.PP...PLRH.DSGERLSNGER
Retrocopy IFELQVYSNNKIALLMNLL*NPNIPPTKIPLRH-DSGERLSNGER

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	4.17 RPM
SRP051959_heart	0.02 RPM	6.49 RPM
SRP051959_kidney	0.00 RPM	8.63 RPM
SRP051959_liver	0.00 RPM	3.53 RPM
SRP051959_lung	0.00 RPM	7.00 RPM
SRP051959_lymph_node	0.00 RPM	7.90 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.03 RPM
SRP051959_spleen	0.02 RPM	6.28 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_464 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_464 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	ENSCJAG00000001118	1 retrocopy	retro_cjac_464 ,