RetrogeneDB ID: retro_cjac_999

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:88856108..88856708(+)
• Located in intron of: ENSCJAG00000017573

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC28B
• Ensembl ID: ENSCJAG00000006747
• Aliases: None
• Description: coiled-coil domain containing 28B [Source:HGNC Symbol;Acc:28163]

Sequence

>retro_cjac_999
ATGGATGACGAGAAGAAGAAACGGAGTCCCAAGCCCTGCCTGGCCCAGCCAGCCCAGGCCCCAGGCACACTACGCAGGGT
CCCTGTGCCTACCAGCCACAGCGGCTCCTTGGCCCTAGGACTTCCTCATCTGCCATCCCCCAAGCAGCGGGCCAAGTTCA
AGAGAGTAGGCAAGGAGAAGTACCGCCCAGTGCTGGCCCGAGGTGGAGGCGGCTCTGCAGGCACGCCCCTGCAGCACTCC
TTCCTGACCGAGGTGACTGATGTCTGTGAGATGGAGGGGGGACTCCTGAACCTGCTCAATGATTTTCAGTCCAGCGGGCT
GAAGGCCTTCGGGAAGGAATGCTCCTTTGAGCAGCTGGAGCACGTTCGGGAGATGCAGGAGAAGCTGGCTCGGCTGCACT
TCAGCCTAGACGTGTGTGGGGAGGAAGAGGATGATGAAGAGGAAGAGGATGGGGTCACTGAGGGGCTGCCGGAGGAGCAG
AAGAAGACGATGGCTGACCGTAACTTGGACCAACTGCTTAGCAATCTGGAAGACCTGAGTAATTCGATCCAGAAGCGGCA
CCTGGCCGAGAACGCCGAGCCTGAGGAGCAGTCTGCTGCG

Alignment

ORF - retro_cjac_999 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDDKKKKRSPKPCLAQPAQAPGTLRRVPVPTSHSGSLALGLPHLPSPKQRAKFKRGTXEKCRPVLAGGGG
          MDD.KKKRSPKPCLAQPAQAPGTLRRVPVPTSHSGSLALGLPHLPSPKQRAKFKR...EK.RPVLA.GGG
Retrocopy MDDEKKKRSPKPCLAQPAQAPGTLRRVPVPTSHSGSLALGLPHLPSPKQRAKFKRVGKEKYRPVLARGGG

Parental  GSACCTPLQHSFLTEVTDVYEMEGGLLNLLNDFHSGRLQAFGKECSFEQLEHVREMQEKLARLHFSLDVC
          GSA..TPLQHSFLTEVTDV.EMEGGLLNLLNDF.S..L.AFGKECSFEQLEHVREMQEKLARLHFSLDVC
Retrocopy GSAG-TPLQHSFLTEVTDVCEMEGGLLNLLNDFQSSGLKAFGKECSFEQLEHVREMQEKLARLHFSLDVC

Parental  GEEEDDEEEEDGVTEGLPEEQKKTMADRNLDQLLSNLEDLSNSIQKLHLAENAEPEEQSAA
          G..........GVTEGLPEEQKKTMADRNLDQLLSNLEDLSNSIQK.HLAENAEPEEQSAA
Retrocopy GXXXXXXXXXXGVTEGLPEEQKKTMADRNLDQLLSNLEDLSNSIQKRHLAENAEPEEQSAA

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	0.64 RPM	0.38 RPM
SRP051959_heart	0.54 RPM	0.53 RPM
SRP051959_kidney	0.44 RPM	0.31 RPM
SRP051959_liver	0.43 RPM	0.17 RPM
SRP051959_lung	0.76 RPM	0.57 RPM
SRP051959_lymph_node	0.43 RPM	0.55 RPM
SRP051959_skeletal_muscle	0.76 RPM	0.98 RPM
SRP051959_spleen	0.95 RPM	0.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_999 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_999 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006747	1 retrocopy	retro_cjac_999 ,