RetrogeneDB ID: retro_cjac_4216

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:111922451..111922683(-)
• Located in intron of: ENSCJAG00000020559

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT4H1
• Ensembl ID: ENSCJAG00000017369
• Aliases: None
• Description: suppressor of Ty 4 homolog 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:11467]

Sequence

>retro_cjac_4216
CTGGAGATGGTACCTAAGGACATGAGGCATCTGTGGGCTTGTTTCCTGTATTTGCTGGTCAAGACTATAGATCAATTTGA
ATATAATGGTTCCGAAAATTGTGATGTATATCTACAGATTAAGGGTAACTGAGAGAGGATTATGTGACTACACCAACTCT
TCCTTTGATGGAATAATTGTAGTGATGAGTCGAGAGGACACCTAGGTCTCCAAGTGGCAGCAAGTCAGTAAC

Alignment

ORF - retro_cjac_4216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 65.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVY-DCTSSSFDGIIAMMSPEDSWV
          LE.VPKD.RHL.AC.L..LVKTIDQFEY.G..NCD.YLQ.KGN.E....D.T.SSFDGII..MS.ED..V
Retrocopy LEMVPKDMRHLWACFLYLLVKTIDQFEYNGSENCDVYLQIKGN*ERIM>DYTNSSFDGIIVVMSREDT*V

Parental  SKWQRVSN
          SKWQ.VSN
Retrocopy SKWQQVSN

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	0.38 RPM	6.77 RPM
SRP051959_heart	0.23 RPM	6.33 RPM
SRP051959_kidney	0.11 RPM	8.32 RPM
SRP051959_liver	0.13 RPM	8.17 RPM
SRP051959_lung	0.49 RPM	9.13 RPM
SRP051959_lymph_node	0.48 RPM	9.89 RPM
SRP051959_skeletal_muscle	0.17 RPM	6.86 RPM
SRP051959_spleen	0.36 RPM	12.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4216 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4216 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017369	3 retrocopies	retro_cjac_1196, retro_cjac_1990, retro_cjac_4216 ,
Dipodomys ordii	ENSDORG00000002826	2 retrocopies	retro_dord_177, retro_dord_220,
Macropus eugenii	ENSMEUG00000010164	1 retrocopy	retro_meug_2079,
Myotis lucifugus	ENSMLUG00000025583	1 retrocopy	retro_mluc_761,
Otolemur garnettii	ENSOGAG00000031972	1 retrocopy	retro_ogar_2702,