RetrogeneDB ID: retro_cjac_1196

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:31182471..31182815(+)
• Located in intron of: ENSCJAG00000017116

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_1196
ATGGCCCTGGAGATGGTGCTGAAGAACTTGCAGCATCTATGGGCTTGTCTGCTGTGTTTGCTGGTCAAGTCTATAGACCA
GTTTGAATATGATGGTTGTGACAACTGTGATCCCTATGTACAGATGAAGAATAATAACCGAGAGATGGTATATGACCACA
CTAGCTCTTCCTTTGATGGAATCATTGCAATGATGAGTCCAGAGGACAGCTAGGTCTCCAAGTGTCAGCTAGTCAGTAAC
TTTAAGCCAGGTGTATATGCAGTGTCATTCACTAGTTGCCTGCCCCAAGGAATCATGTGGAAGTGAAAAGTCGAGGAGTG
ATCTCCAAATCCAGAGACACAGCT

Alignment

ORF - retro_cjac_1196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.31 %
• Parental protein coverage: 97.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGN-REMVYDCTSSSFDGIIAMMSPEDS
          MALE.V.K.L.HL.ACLLC.LVK.IDQFEYDGCDNCD.Y.QMK.N.REMVYD.TSSSFDGIIAMMSPEDS
Retrocopy MALEMVLKNLQHLWACLLCLLVKSIDQFEYDGCDNCDPYVQMKNNNREMVYDHTSSSFDGIIAMMSPEDS

Parental  WVSKWQRVSNFKPGVYAVSVTGRLPQGIV-RELKSRGVAYKSRDTA
          .VSK.Q.VSNFKPGVYAVS.T..LPQGI...E.KSRGV..KSRDTA
Retrocopy *VSKCQLVSNFKPGVYAVSFTSCLPQGIM<VEVKSRGVISKSRDTA

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	0.29 RPM	6.77 RPM
SRP051959_heart	0.21 RPM	6.33 RPM
SRP051959_kidney	0.29 RPM	8.32 RPM
SRP051959_liver	0.17 RPM	8.17 RPM
SRP051959_lung	0.26 RPM	9.13 RPM
SRP051959_lymph_node	0.53 RPM	9.89 RPM
SRP051959_skeletal_muscle	0.07 RPM	6.86 RPM
SRP051959_spleen	0.38 RPM	12.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1196 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1196 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2280
Pan troglodytes	retro_ptro_1614
Gorilla gorilla	retro_ggor_1693
Pongo abelii	retro_pabe_1940

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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,