RetrogeneDB ID: retro_cjac_2655

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:108750053..108750448(-)
• Located in intron of: ENSCJAG00000007395

Retrocopy information

• Ensembl ID: ENSCJAG00000007393
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000002320
• Aliases: None
• Description: None

Sequence

>retro_cjac_2655
ACGGAGAGTCCCTGGATGGTCGTCAGATCCTTGTGGATCACGCAGGCAAGTCTGCTCGGGGAACTAGAGGAGGTGCCTTT
GGGGCCCATGGGCGTGGTTGCAGCTACTCTAGAGGTGGTGGGGACCAGGGCTATGGGAGTGGCAGGTATTACGACAGTCG
ACCTGGAGGGTATGGATATGGATATGGACGTTCCAGTTCCAGAGACTATAATGGCAGAACCAGGGTGGTTATGACCGCTA
CTCAGGAGGAAATTATAGAGACAATTATGACAACTGAAATGAGACATGCACATAATGTAGATACACAAGGAATAATTTTT
GATCCAGGATCGTCCTTCCAAATGGCCGTATTTATAAAGGTTTTTGGAGCTACACTGAAACATCTTATTTTACAG

Alignment

ORF - retro_cjac_2655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.98 %
• Parental protein coverage: 76.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TRSLWMVVRSVWITQASLLGELEEVPLGSMGVVAATLEVVGTRAMGVAGIMTVDLEGMDMDMDVPVPETI
          T.S.WMVVRS.WITQASLLGELEEVPLG.MGVVAATLEVVGTRAMGVAGI.TVDLEGMDMDMDVPVPETI
Retrocopy TESPWMVVRSLWITQASLLGELEEVPLGPMGVVAATLEVVGTRAMGVAGITTVDLEGMDMDMDVPVPETI

Parental  MAE-TRVVMTATQGEIIETITTTEMRHAHNVDTQGIIFDPGSSFQMAVFIKVFGATLKHLILQ
          MAE.TRVVMTATQ.EIIETI.TTEMRHAHNVDTQGIIFDPGSSFQMAVFIKVFGATLKHLILQ
Retrocopy MAE<TRVVMTATQEEIIETIMTTEMRHAHNVDTQGIIFDPGSSFQMAVFIKVFGATLKHLILQ

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	0.04 RPM	33.10 RPM
SRP051959_heart	0.07 RPM	32.48 RPM
SRP051959_kidney	0.04 RPM	35.56 RPM
SRP051959_liver	0.06 RPM	42.37 RPM
SRP051959_lung	0.18 RPM	41.25 RPM
SRP051959_lymph_node	0.07 RPM	53.56 RPM
SRP051959_skeletal_muscle	0.04 RPM	34.98 RPM
SRP051959_spleen	0.06 RPM	61.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2655 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2655 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002320	1 retrocopy	retro_cjac_2655 ,
Echinops telfairi	ENSETEG00000001939	6 retrocopies	retro_etel_1057, retro_etel_1060, retro_etel_1209, retro_etel_1476, retro_etel_169, retro_etel_531,
Microcebus murinus	ENSMICG00000014371	5 retrocopies	retro_mmur_1450, retro_mmur_878, retro_mmur_957, retro_mmur_958, retro_mmur_998,
Macaca mulatta	ENSMMUG00000004439	1 retrocopy	retro_mmul_455,
Sorex araneus	ENSSARG00000003340	1 retrocopy	retro_sara_45,
Tupaia belangeri	ENSTBEG00000003499	10 retrocopies	retro_tbel_100, retro_tbel_1589, retro_tbel_1774, retro_tbel_1779, retro_tbel_1869, retro_tbel_2829, retro_tbel_3822, retro_tbel_3999, retro_tbel_4268, retro_tbel_427,