RetrogeneDB ID: retro_cjac_1178

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:4548787..4549128(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB31
• Ensembl ID: ENSCJAG00000004529
• Aliases: None
• Description: RAB31, member RAS oncogene family [Source:HGNC Symbol;Acc:9771]

Sequence

>retro_cjac_1178
ATAACAGTGCATGATGTTACCCAAACAGGATTCATTTCATACCTTGAAGAAGTGGGATGAAGAGCTGAAAGAACATGGTC
CGGAAAACATCCAAATGGTTATTGCCGAAACAAGTGCCACCTCTCAGATATTAGGGAGATTTTCCTGAAGGATGCTGAGG
AATATGCTGAATTCATAGGTGCCATCAGTGGTTGAGGCAAGGGCAAAAAAATCCTATTAATATTGAAGAGCTCTTTCAAG
GTATCAGCCACCAGATCCCAGCCTTGGACCCCCATGAAAATGGAAACAATGGAGTGAGGAGACTCGGGGAGCAAACCATG
CAAGCCAGCCTCAGATGTTGT

Alignment

ORF - retro_cjac_1178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.65 %
• Parental protein coverage: 57.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VIVYDIT-KQDSFYTLKKWVKELKEHGPENIVMAIAG-NKCDLSDIREVPLKDAKEYAESIGAI-VVETS
          ..V.D.T.KQDSF.TLKKW..ELKEHGPENI.M.IA..NKC.LSDIRE..LKDA.EYAE.IGAI.VVE..
Retrocopy ITVHDVT>KQDSFHTLKKWDEELKEHGPENIQMVIAE<NKCHLSDIREIFLKDAEEYAEFIGAI>VVEAR

Parental  AK-NAINIEELFQGISRQIPPLDHHENGNNGAIKLVKQTTQASRRCC
          AK.N.INIEELFQGIS.QIP.LD.HENGNNG...L..QT.QAS.RCC
Retrocopy AK>NPINIEELFQGISHQIPALDPHENGNNGVRRLGEQTMQASLRCC

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	25.12 RPM
SRP051959_heart	0.00 RPM	43.43 RPM
SRP051959_kidney	0.00 RPM	33.30 RPM
SRP051959_liver	0.00 RPM	41.63 RPM
SRP051959_lung	0.00 RPM	68.62 RPM
SRP051959_lymph_node	0.00 RPM	19.25 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.29 RPM
SRP051959_spleen	0.00 RPM	64.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1178 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Callithrix jacchus	ENSCJAG00000004529	2 retrocopies	retro_cjac_1178 , retro_cjac_1179,
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Callithrix jacchus	ENSCJAG00000019039	2 retrocopies	retro_cjac_1715, retro_cjac_842,
Microcebus murinus	ENSMICG00000002882	1 retrocopy	retro_mmur_1453,
Macaca mulatta	ENSMMUG00000005692	1 retrocopy	retro_mmul_1557,
Monodelphis domestica	ENSMODG00000021443	3 retrocopies	retro_mdom_1491, retro_mdom_1766, retro_mdom_994,
Pteropus vampyrus	ENSPVAG00000016514	1 retrocopy	retro_pvam_874,