RetrogeneDB ID: retro_cjac_2373

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:118476835..118477239(+)
• Located in intron of: ENSCJAG00000004178

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014776
• Aliases: None
• Description: None

Sequence

>retro_cjac_2373
ATGAATGGCAACAGCACCTTTGCAAAGAGTCCCAGGGATGATGCTCAGATATCAAAGAAGAGACACACAGCCTTCAATGT
TACTGTCAGATACTTCTCTAAGAAGAATTGGGAAAAGCTGAAAAACTCAAAGAAAATCACCCATGGGTATATGAAGAGAA
ACATGAGACCATGACTAAACTAGGTATCAAGGCCACTCTCCCAACTTTCATGTATAATAAATGGGCCACAGACCTCCAGG
GGAATGATTCTGATAGACACCATAGCTGTGGGAATCAGGATGAACATCCTCAGATGGCTTTCGGCTTGCTATAAGGGAAC
TTTCCAAAGATGATGCCCAAGAAGCCAGCAGAGGAAGGAAATTATTCAAAGGGAGTGCCAGAAGCATCTGTCTCACAAAA
CGAT

Alignment

ORF - retro_cjac_2373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.55 %
• Parental protein coverage: 72.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNGDGSFAKNPSDDEQISENKRKAFADIAQYFSKKDWKKLKYSEKITYVYMKRN-YEAMRTLGFQVTIPL
          MNG...FAK.P.DD.QIS.....AF.....YFSKK.W.KLK.S.KIT..YMKRN..E.M..LG...T.P.
Retrocopy MNGNSTFAKSPRDDAQISKKRHTAFNVTVRYFSKKNWEKLKNSKKITHGYMKRN<HETMTKLGIKATLPT

Parental  FMRDKQAEDSQEDDSDRDSNPGNLLECHTMTFGMFQGLFPQIMPREPPEEEGNDSEAVPETSGTQND
          FM..K.A.D.Q..DSDR....GN..E...M.FG...G.FP..MP...P.EEGN.S..VPE.S..QND
Retrocopy FMYNKWATDLQGNDSDRHHSCGNQDEHPQMAFGLL*GNFPKMMPKK-PAEEGNYSKGVPEASVSQND

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	0.58 RPM	0.00 RPM
SRP051959_heart	17.70 RPM	0.00 RPM
SRP051959_kidney	0.87 RPM	0.00 RPM
SRP051959_liver	0.22 RPM	0.00 RPM
SRP051959_lung	1.30 RPM	0.00 RPM
SRP051959_lymph_node	1.32 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.96 RPM	0.00 RPM
SRP051959_spleen	1.43 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2373 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2373 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3512
Pan troglodytes	retro_ptro_2385
Gorilla gorilla	retro_ggor_2374
Pongo abelii	retro_pabe_2903
Macaca mulatta	retro_mmul_1862

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014776	1 retrocopy	retro_cjac_2373 ,
Homo sapiens	ENSG00000204645	1 retrocopy	retro_hsap_3512,
Gorilla gorilla	ENSGGOG00000026107	1 retrocopy	retro_ggor_2374,
Macaca mulatta	ENSMMUG00000019164	1 retrocopy	retro_mmul_1862,
Nomascus leucogenys	ENSNLEG00000003504	1 retrocopy	retro_nleu_482,
Pongo abelii	ENSPPYG00000020365	1 retrocopy	retro_pabe_2903,
Pan troglodytes	ENSPTRG00000021857	1 retrocopy	retro_ptro_2385,
Ictidomys tridecemlineatus	ENSSTOG00000015375	3 retrocopies	retro_itri_1394, retro_itri_1855, retro_itri_746,