RetrogeneDB ID: retro_cjac_2434

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:43055322..43055676(-)
• Located in intron of: ENSCJAG00000004251

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDTL
• Ensembl ID: ENSCJAG00000009483
• Aliases: None
• Description: D-dopachrome tautomerase-like [Source:HGNC Symbol;Acc:33446]

Sequence

>retro_cjac_2434
ATGCCATTTCTAGAGCTGGACATGAATTTGCTTGCAAACCAAGTGCCCATGGGGCTGGAGAAATGACTCTGCAATGCTGC
TGCCTCCATCCTGGGCAAACCTGTGGACCGCGTGAATGTGACTGTGTGGCTGGGCCTGGTCATGGCGCTGAGTGGGTCCA
CTGAGCCCTGCGCACAGCCGTCCGTCTCCTTCATTGGCATAGTGGGCACCTCTGAGGACCACCGCAAACACAGTGCCCAC
TTCTTTGAGTTTCTCACCAAGGGGCTAGCTCCAGAGCAGGACAGGATAATTATTTGCTTTTTACCCCTGGAGCCCTGGCA
GATTGGCAAGAAAGGGACAGTCATGACTTTTTTA

Alignment

ORF - retro_cjac_2434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTMRPGLAMSLNGSTEPCAQLSVSSIGVVGT
          MPFLELD.NL.AN.VP.GLEK.LC.AAASILGKP.DRVNVT...GL.M.L.GSTEPCAQ.SVS.IG.VGT
Retrocopy MPFLELDMNLLANQVPMGLEK*LCNAAASILGKPVDRVNVTVWLGLVMALSGSTEPCAQPSVSFIGIVGT

Parental  AEDNRSHSAHFFEFLTKELALDQDRILIRFFPLEPWQIGKKGTVMTFL
          .ED.R.HSAHFFEFLTK.LA..QDRI.I.F.PLEPWQIGKKGTVMTFL
Retrocopy SEDHRKHSAHFFEFLTKGLAPEQDRIIICFLPLEPWQIGKKGTVMTFL

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	0.11 RPM	12.36 RPM
SRP051959_heart	0.07 RPM	8.95 RPM
SRP051959_kidney	0.04 RPM	12.56 RPM
SRP051959_liver	0.15 RPM	68.12 RPM
SRP051959_lung	0.23 RPM	8.87 RPM
SRP051959_lymph_node	0.14 RPM	6.89 RPM
SRP051959_skeletal_muscle	0.17 RPM	12.91 RPM
SRP051959_spleen	0.13 RPM	7.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2434 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2434 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2434 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013811	1 retrocopy	retro_amel_1024,
Callithrix jacchus	ENSCJAG00000009483	1 retrocopy	retro_cjac_2434 ,
Felis catus	ENSFCAG00000009408	1 retrocopy	retro_fcat_1172,
Mustela putorius furo	ENSMPUG00000002935	1 retrocopy	retro_mputfur_1365,