RetrogeneDB ID: retro_cjac_2504

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:19704412..19704978(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIMP1
• Ensembl ID: ENSCJAG00000015885
• Aliases: None
• Description: aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 [Source:HGNC Symbol;Acc:10648]

Sequence

>retro_cjac_2504
CAGGAGAAGAAAAGAAAGCAAAAGAGATAATTGAAAGGAGAGAAGAAGGAGAAAAAATAGCAATCAATAGCAGGAAGCAC
CAGCTCTAAGCCAATAGATGTTTTCCATGTAGATCTTTGAACTGGTGGCATCATAAATGTCAGAAAACACCCTGATGCAG
ATTCTTTGTATGTAGAAGACATTGTGGTTGGGGAAATAGTCTCAAGAATAGTTGTTAGTGGTCTGGAGAATCATGTTCTT
CTTGAACAGATGCAAAATCAGATAGTGATTTTACTTTGTAACCTGAAACCTGTAAAGATGAGGGGAGTATTATTTCAAGC
AGTGGTCATGTGTGTTTTTTCACCAGAGAAAATTGAAATCTTGGCCCCTCCTAATGCAGACAGATTTACTTTTGATGCTT
TCCCTGGAGAGCCCAACAAGGAACCAAATCCTAAGAAGATTTGGGAGCAGATCCCATCTCATCTTTATACTATGATGAGT
GTGTGGCTACATACAAAGGAGCTTCCTTTAAGTTGAAAGGGAAGGAGGTTTGTAGGGTTCAAACCATGAACAACAGTGGA
ATAAAA

Alignment

ORF - retro_cjac_2504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.72 %
• Parental protein coverage: 57.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEKKAKEKTENKVEKKEKKQQSVAGSTNSSPIDVSRLDLRIGCIITAKKHPDADSLYVEEVDVGEITPRT
          .EKK.K.K...K.EKKEKK.QS.AGST.S.PIDV...DL..G.II...KHPDADSLYVE...VGEI..R.
Retrocopy QEKKRKQKR*LKGEKKEKK*QSIAGSTSSKPIDVFHVDL*TGGIINVRKHPDADSLYVEDIVVGEIVSRI

Parental  VVSGLVNHVPLEQMQNRMVVLLCNLKPAKMRGVLSQAMVMCASSPEKVEILAPPNGSVPGDRITFAAFPG
          VVSGL.NHV.LEQMQN..V.LLCNLKP.KMRGVL.QA.VMC..SPEK.EILAPPN.....DR.TF.AFPG
Retrocopy VVSGLENHVLLEQMQNQIVILLCNLKPVKMRGVLFQAVVMCVFSPEKIEILAPPN----ADRFTFDAFPG

Parental  VPDKELNPKKKIWEQIQPDLHT-NDECVATYKGVPFEVKGKGVCRAQTMSNSGIK
          .P.KE.NP.KKIWEQI...L.T..DECVATYKG..F..KGK.VCR.QTM.NSGIK
Retrocopy EPNKEPNP-KKIWEQIPSHLYT<YDECVATYKGASFKLKGKEVCRVQTMNNSGIK

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	0.16 RPM	9.45 RPM
SRP051959_heart	0.70 RPM	18.68 RPM
SRP051959_kidney	0.31 RPM	14.22 RPM
SRP051959_liver	0.13 RPM	23.11 RPM
SRP051959_lung	0.31 RPM	11.79 RPM
SRP051959_lymph_node	0.41 RPM	12.58 RPM
SRP051959_skeletal_muscle	0.20 RPM	39.31 RPM
SRP051959_spleen	0.19 RPM	13.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2504 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2504 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1780

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000619	2 retrocopies	retro_chof_1176, retro_chof_2050,
Callithrix jacchus	ENSCJAG00000015885	1 retrocopy	retro_cjac_2504 ,
Dipodomys ordii	ENSDORG00000005018	1 retrocopy	retro_dord_540,
Mustela putorius furo	ENSMPUG00000008952	1 retrocopy	retro_mputfur_1606,
Mus musculus	ENSMUSG00000028029	2 retrocopies	retro_mmus_2271, retro_mmus_3334,
Pongo abelii	ENSPPYG00000014981	1 retrocopy	retro_pabe_1780,
Rattus norvegicus	ENSRNOG00000011384	1 retrocopy	retro_rnor_1704,
Ictidomys tridecemlineatus	ENSSTOG00000008178	1 retrocopy	retro_itri_1173,
Tupaia belangeri	ENSTBEG00000004412	1 retrocopy	retro_tbel_4008,