RetrogeneDB ID: retro_cjac_1535

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:9608677..9609068(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000033929
• Aliases: None
• Description: None

Sequence

>retro_cjac_1535
GGTGAAGATGAACAAGAAGGCACAAATCCACACTTGCCAATGGACCCGAGTGATAACAACAAACCCAGTGACACCTGTCT
AGTGCTGGCGCTTAAAGTCAGAATTCAGAGCCCCAGAGAAATGACTTCATTGAAATTGAACTGAAGAGACAAGAACTGAG
TTACCAAAACTTACTAAAAGTGAGTTGCTGTGAACTGCGGATTAACCCAGAGCAAGTGGAGAAGATCAGAGCTACCAAAT
CCCTGCTCAGAAAGGACCAAGACATTCCAAGACTGCGGGACTTTCAGGAAGTAGAACTCATTTTAATGAAAAATGGAAGC
TCCGAATTGACAGAGTCTATACCGTCTCTGACAGACCCTGCTACAATAGCAAAGCTGCAAAATTGAATTAC

Alignment

ORF - retro_cjac_1535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.75 %
• Parental protein coverage: 91.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GEDKQEGTNPYLPMDPSDNNKPSDTCLELVLKVRIQSPKE-NDFIEIELKRQELSYQNLLKVSCCELGIN
          GED.QEGTNP.LPMDPSDNNKPSDTCL.L.LKVRIQSP.E.NDFIEIELKRQELSYQNLLKVSCCEL.IN
Retrocopy GEDEQEGTNPHLPMDPSDNNKPSDTCLVLALKVRIQSPRE<NDFIEIELKRQELSYQNLLKVSCCELRIN

Parental  PEQVEKIRKLPNTLLRKIKDQDIQRLRDFQEVELILMKNGSSELTEYIPSLTERPCYNSK-AAKMTY
          PEQVEKIR.....LLR..KDQDI.RLRDFQEVELILMKNGSSELTE.IPSLT..P....K.AAK..Y
Retrocopy PEQVEKIR-ATKSLLR--KDQDIPRLRDFQEVELILMKNGSSELTESIPSLTD-PATIAK<AAKLNY

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	0.40 RPM	3.15 RPM
SRP051959_heart	0.61 RPM	0.18 RPM
SRP051959_kidney	1.66 RPM	0.04 RPM
SRP051959_liver	0.00 RPM	0.06 RPM
SRP051959_lung	0.60 RPM	0.20 RPM
SRP051959_lymph_node	0.00 RPM	0.39 RPM
SRP051959_skeletal_muscle	0.13 RPM	0.07 RPM
SRP051959_spleen	0.32 RPM	0.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1535 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1535 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025183	1 retrocopy	retro_btau_858,
Callithrix jacchus	ENSCJAG00000033929	1 retrocopy	retro_cjac_1535 ,