RetrogeneDB ID: retro_cjac_2032

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:37513880..37514228(+)
• Located in intron of: ENSCJAG00000003083

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019406
• Aliases: None
• Description: None

Sequence

>retro_cjac_2032
ATGGGGCTGTTTGGAAAAACCCAGGAGAAGCCACTTAAAGAACTGATCCATGAATGGTCATTGAAGATAAGAAAGGAAAT
GAGAGTTGTTGACAGGCAAATAAGGGATATCCAAAGAGAAGAAGAAAAAGTGAAACAATCTGTGAAAGATGCAGCCAAGA
AGGGCCAGAATGATGTCCGTGTAGTTCTGACCAAGGAGATGATCAGGTCAAGGAAGGCCATGAGCAAGCGGTATGCATCC
AAAGTGCACATGAACTCAGTGCTCATGGGGATGAAGAACCAGCTCATGGTCTTGTGAGTGGCTGGTTCCCTGCAGAAGAG
CACAGAAGTGATGAAGGCCATGCAGTCT

Alignment

ORF - retro_cjac_2032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 52.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVVLAKEMIRS
          MGLFGKTQEKP.KEL..EWSLKIRKEMRVVDRQIRDIQREEEKVK.SVKDAAKKGQ.DV.VVL.KEMIRS
Retrocopy MGLFGKTQEKPLKELIHEWSLKIRKEMRVVDRQIRDIQREEEKVKQSVKDAAKKGQNDVRVVLTKEMIRS

Parental  RKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQS
          RKA.SK.YASK.HMNSVLMGMKNQL.VL.VAGSLQKSTEVMKAMQS
Retrocopy RKAMSKRYASKVHMNSVLMGMKNQLMVL*VAGSLQKSTEVMKAMQS

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	0.24 RPM	31.42 RPM
SRP051959_heart	0.18 RPM	29.06 RPM
SRP051959_kidney	0.44 RPM	34.23 RPM
SRP051959_liver	0.22 RPM	18.65 RPM
SRP051959_lung	0.31 RPM	28.70 RPM
SRP051959_lymph_node	0.53 RPM	16.76 RPM
SRP051959_skeletal_muscle	0.22 RPM	21.07 RPM
SRP051959_spleen	0.34 RPM	29.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2032 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2032 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007479	1 retrocopy	retro_cfam_1869,
Callithrix jacchus	ENSCJAG00000019406	2 retrocopies	retro_cjac_2032 , retro_cjac_2784,
Cavia porcellus	ENSCPOG00000001723	1 retrocopy	retro_cpor_920,
Macropus eugenii	ENSMEUG00000009111	1 retrocopy	retro_meug_178,
Microcebus murinus	ENSMICG00000005492	3 retrocopies	retro_mmur_1110, retro_mmur_1396, retro_mmur_47,
Mus musculus	ENSMUSG00000053119	1 retrocopy	retro_mmus_1683,
Oryctolagus cuniculus	ENSOCUG00000029277	1 retrocopy	retro_ocun_1044,
Ochotona princeps	ENSOPRG00000002191	2 retrocopies	retro_opri_18, retro_opri_436,
Sorex araneus	ENSSARG00000008917	1 retrocopy	retro_sara_13,
Tursiops truncatus	ENSTTRG00000010400	1 retrocopy	retro_ttru_638,