RetrogeneDB ID: retro_cjac_1677

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:27654640..27655031(-)
• Located in intron of: ENSCJAG00000008147

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM50A
• Ensembl ID: ENSCJAG00000018575
• Aliases: None
• Description: transmembrane protein 50A [Source:HGNC Symbol;Acc:30590]

Sequence

>retro_cjac_1677
GGCGGGAAGGGCAATAGGATTGCTTCCACTGCTGCTGGTGTACTATTTTTTACAGGCTGGGGGATTATCATAGATGCAGC
TGTCATTTATTCCCCCATGGACGATTTCAACCACTCGTACCATGCCTGTGGTGTTTAAGAAACCATAGCCTTCCTAATAA
TTAATGCAGTATCGAGTGGACAAGTCCCAGGTGATAGTTAACGCTGAAGGTTGGCTGGGTCAAACAGGTGCTGCTATCTG
GCTGTTTATTGGTTTCATGTTGGCCTTTGGATCTCTGATTGCATCTATGTGGATTATTTTTGGAGGTTATGTTGCTAAAG
AAAAAGTTGTAGTATCCCCTGGAATTGCTGTGTTTATCCAGAACACCCTCATCTTTTTTGGAGGGCTGGTT

Alignment

ORF - retro_cjac_1677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.97 %
• Parental protein coverage: 82.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GEKRNTIASIAAGVLFFTGWWIIIDAAVIYSPMEDFNHSYHACGVIATIAFLMINAVSNGQVRGDS-YSE
          G.K.N.IAS.AAGVLFFTGW.IIIDAAVIYSPM.DFNHSYHACGV..TIAFL.INAVS.GQV.GDS...E
Retrocopy GGKGNRIASTAAGVLFFTGWGIIIDAAVIYSPMDDFNHSYHACGV*ETIAFLIINAVSSGQVPGDS>NAE

Parental  GCLGQTGARIWLFIGFMLAFGSLIASMWILFGGYVAKEKVVVYPGIAVFFQNAFIFFGGLV
          G.LGQTGA.IWLFIGFMLAFGSLIASMWI.FGGYVAKEKVVV.PGIAVF.QN..IFFGGLV
Retrocopy GWLGQTGAAIWLFIGFMLAFGSLIASMWIIFGGYVAKEKVVVSPGIAVFIQNTLIFFGGLV

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	16.26 RPM
SRP051959_heart	0.00 RPM	16.19 RPM
SRP051959_kidney	0.00 RPM	28.00 RPM
SRP051959_liver	0.00 RPM	17.33 RPM
SRP051959_lung	0.03 RPM	23.08 RPM
SRP051959_lymph_node	0.00 RPM	27.88 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.25 RPM
SRP051959_spleen	0.00 RPM	21.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1677 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1677 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1677 has 0 orthologous retrocopies within eutheria group .

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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	ENSCJAG00000018575	1 retrocopy	retro_cjac_1677 ,
Cavia porcellus	ENSCPOG00000012615	1 retrocopy	retro_cpor_707,
Echinops telfairi	ENSETEG00000007483	1 retrocopy	retro_etel_2061,
Macropus eugenii	ENSMEUG00000002060	1 retrocopy	retro_meug_1270,
Macaca mulatta	ENSMMUG00000032217	1 retrocopy	retro_mmul_1408,
Ochotona princeps	ENSOPRG00000001182	2 retrocopies	retro_opri_546, retro_opri_62,
Pongo abelii	ENSPPYG00000001711	1 retrocopy	retro_pabe_1679,
Ictidomys tridecemlineatus	ENSSTOG00000022246	2 retrocopies	retro_itri_1228, retro_itri_1329,