RetrogeneDB ID: retro_cjac_2774

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:140245811..140246401(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLX
• Ensembl ID: ENSCJAG00000005011
• Aliases: None
• Description: None

Sequence

>retro_cjac_2774
AAGGCGGAATACGTCTACAGCTACAAAAGCTCAGACCTCACGTTTTTTTATAGAAAGTGCCCACAGTGCCACAATGGAAG
GGTAGTGTCTAGAGCTAATAGCATCAGTTTCACCAGTGCCTCTTCCGTCCCCAACACAGATAAGGACAGAGATTACTACC
AGGAGTCCTACAAGGACCGGTAGTGGTGATCACACACTGAGGCTGAGCAGAAGAAGGACGTCATCAAGAGAGACTGTGAT
GATCTTCAGACCATCGTCCCCCACTGCCAGCAGCAGGACTTCTGTATTGGCTCCCAAAAGCTCAGCAAAACCATCGTTCT
ACAAAAGACCATTGACTACACTCATTTGCACAAGGAGAAGAAAACACAGGAGGAAGTGTCCACACTACGCTAGGACATCA
CAGCCCTAAAAATCATGAAAATGAACGATGAACAGATGGTGGAGGCACACCAGGACATCCCCATGAGAGGGAGGACCAGG
CCTCTGACCAAGTCAAGATCAACGTGTTTTGAGGTATCCTGGACTCACTGTTTTGTTCCTTCAACACCTTCGTCTCTGTG
ACCAACTTCCAGGAGCTGTCAGACTGTCTT

Alignment

ORF - retro_cjac_2774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.96 %
• Parental protein coverage: 67.79 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVEYAYSDNSLDPGLFVEST---RKGSVVSRANSIGSTSASSVPNTDDEDSDYHQEAYKESYKDRRRRAH
          K.EY.YS..S.D...F.........G.VVSRANSI..TSASSVPNTD..D.DY....Y.ESYKDR....H
Retrocopy KAEYVYSYKSSDLTFFYRKCPQCHNGRVVSRANSISFTSASSVPNTD-KDRDY----YQESYKDR*W*SH

Parental  TQAEQKRRDAIKRGYDDLQTIVPTCQQQDFSIGSQKLSKAIVLQKTIDYIQFLHKEKKKQEEEVSTLRKD
          T.AEQK..D.IKR..DDLQTIVP.CQQQDF.IGSQKLSK.IVLQKTIDY...LHKEKK.Q.EEVSTLR.D
Retrocopy TEAEQKK-DVIKRDCDDLQTIVPHCQQQDFCIGSQKLSKTIVLQKTIDYTH-LHKEKKTQ-EEVSTLR*D

Parental  VTALKIMKVNYEQIVKAHQD-NPHEGEDQVSDQVKFNVFQGIMDSLFQSFNASISVTSFQELSACV
          .TALKIMK.N.EQ.V.AHQD..PHE.EDQ.SDQVK.NVF.GI.DSLF.SFN...SVT.FQELS.C.
Retrocopy ITALKIMKMNDEQMVEAHQD<HPHEREDQASDQVKINVF*GILDSLFCSFNTFVSVTNFQELSDCL

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	0.02 RPM	7.26 RPM
SRP051959_heart	0.04 RPM	7.65 RPM
SRP051959_kidney	0.04 RPM	9.03 RPM
SRP051959_liver	0.00 RPM	8.97 RPM
SRP051959_lung	0.03 RPM	8.33 RPM
SRP051959_lymph_node	0.05 RPM	10.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.28 RPM
SRP051959_spleen	0.04 RPM	9.43 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2774 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2774 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005011	1 retrocopy	retro_cjac_2774 ,
Homo sapiens	ENSG00000108788	1 retrocopy	retro_hsap_2216,
Gorilla gorilla	ENSGGOG00000010869	1 retrocopy	retro_ggor_1748,
Microcebus murinus	ENSMICG00000010258	1 retrocopy	retro_mmur_1373,
Monodelphis domestica	ENSMODG00000014918	2 retrocopies	retro_mdom_501, retro_mdom_539,
Nomascus leucogenys	ENSNLEG00000011638	1 retrocopy	retro_nleu_2338,
Pongo abelii	ENSPPYG00000008387	1 retrocopy	retro_pabe_2087,
Pan troglodytes	ENSPTRG00000009208	1 retrocopy	retro_ptro_1681,