RetrogeneDB ID: retro_cjac_597

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:102790711..102790905(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YPEL1
• Ensembl ID: ENSCJAG00000015755
• Aliases: None
• Description: yippee-like 1 (Drosophila) [Source:HGNC Symbol;Acc:12845]

Sequence

>retro_cjac_597
GTGATAAAAATGACAAACTCAATAACTTTCCCAGGTTATCTGCCAAATTGTCACTGAATTTATTGCTGTCTCCACTGCAA
ACCTCATTTAGCAAATCATGCTCTGTTGATCTTCAAGTTATCTTGTGTTAGTCAAAACAAAGATTGCCTCTTTAATTCTG
GGAGAATGTAGGCTGTGGCTCAGCAGAGGGGAGG

Alignment

ORF - retro_cjac_597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.58 %
• Parental protein coverage: 54.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVKMTKSKTFQAYLPNCHRTYSCIHCRAHLANHDELISKSFQGSQGRAYLFNS-VVNVGCGPAEER
          ..KMT.S.TF..YLPNCH..Y.C.HC..HLANH..LI.K....SQ....LFNS...NVGCG.AE.R
Retrocopy VIKMTNSITFPGYLPNCH*IYCCLHCKPHLANHALLIFKLSCVSQNKDCLFNS<WENVGCGSAEGR

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	1.77 RPM
SRP051959_heart	0.00 RPM	3.82 RPM
SRP051959_kidney	0.02 RPM	2.26 RPM
SRP051959_liver	0.00 RPM	1.58 RPM
SRP051959_lung	0.00 RPM	4.42 RPM
SRP051959_lymph_node	0.00 RPM	5.64 RPM
SRP051959_skeletal_muscle	0.02 RPM	2.01 RPM
SRP051959_spleen	0.00 RPM	3.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_597 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_597 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_597 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_616

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001397	1 retrocopy	retro_acar_93,
Callithrix jacchus	ENSCJAG00000015755	1 retrocopy	retro_cjac_597 ,
Dasypus novemcinctus	ENSDNOG00000024482	1 retrocopy	retro_dnov_13,
Echinops telfairi	ENSETEG00000008187	1 retrocopy	retro_etel_1965,
Pteropus vampyrus	ENSPVAG00000013638	1 retrocopy	retro_pvam_162,
Tursiops truncatus	ENSTTRG00000016725	1 retrocopy	retro_ttru_1895,