RetrogeneDB ID: retro_cjac_508

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:16860347..16861076(-)
• Located in intron of: ENSCJAG00000021057

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGAT4B
• Ensembl ID: ENSCJAG00000010124
• Aliases: None
• Description: mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B [Source:HGNC Symbol;Acc:7048]

Sequence

>retro_cjac_508
GGGAAGATGTTCAAGTCAGACCTGAGCTTGATTGTAGAGTTCATCCTCATGTTATACCGACACAAGTCCACCGACTGGCC
CCTGGGCCATATTCTGTGGGTGAAAGTCTGCAGCCCCGAGAAGGATGCGAAGCCCTGTGACCGGCAGAAAGCCAACCTGC
GGATCCGCTTCGAGTTGCCCCTATTCCAGCGCGTGGGTACTCACTCCTCACTGGCTGGCAAGATCCAGAAACTGAAGGAC
AAGGACTTTGGAAAGCGGGCACTGCGGAAGGAGCACGTGAGCTCACCAGCAGAGGTGGGCACAAGCCTGAAGACACACCA
GCACTTCACCTGGGAGAAAGCCTACCTACGCGAGGACTTCTGGCCCTTCACCCTCGCCGCTGGGAACTTCATCCGCTTCC
ATTTCTTCCAGCCCTTGCGACTGGAGCAGTTTTTCTTCTGCAGTGGAAACATTGAGCAACCAGAGGACAAGTTCTTCAAT
ACGCCTGTGGAGGTATTGCTCTTTGATAACCCTCAGTCGGATAAGGAGGCCCTGCAGAAGGGCCTCGCCGCCACCCTCCG
GTACCCTCGGAGCCCCAACGGCTACCTCCAGATCGGCTCCTTCTACAAGGGAGTGGCAGAGGGAGAGGTGGGCCCAGCCT
TCGGCCCTCTGGAAGCTCTGCGCCTCTCCATCCAGACGGACTCCCCTGTGTGGGTGATTCTGAGTGAGAGCTTCCTGAAA
AAGGCCGAT

Alignment

ORF - retro_cjac_508 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 50.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKMFKSLDLSLIVEFILMFYRDKPIDWLLDHILWVKVCNPEKDAKHCDRQKANLRIRFKPSLFQHVGTHS
          GKMFKS.DLSLIVEFILM.YR.K..DW.L.HILWVKVC.PEKDAK.CDRQKANLRIRF...LFQ.VGTHS
Retrocopy GKMFKS-DLSLIVEFILMLYRHKSTDWPLGHILWVKVCSPEKDAKPCDRQKANLRIRFELPLFQRVGTHS

Parental  SLAGKIQKLKDKDFGKQALRKEHVNPPAEVSTSLKTYQHFTLEKAYLREDFFWAFTPAAGDFIRFRFFQP
          SLAGKIQKLKDKDFGK.ALRKEHV..PAEV.TSLKT.QHFT.EKAYLREDF.W.FT.AAG.FIRF.FFQP
Retrocopy SLAGKIQKLKDKDFGKRALRKEHVSSPAEVGTSLKTHQHFTWEKAYLREDF-WPFTLAAGNFIRFHFFQP

Parental  LRLERFFFRSGNIEHPEDKLFNTSVEVLPFDNPQSDKEALQEGRAATLRYPRSPDGYLQIGSFYKGVAEG
          LRLE.FFF.SGNIE.PEDK.FNT.VEVL.FDNPQSDKEALQ.G.AATLRYPRSP.GYLQIGSFYKGVAEG
Retrocopy LRLEQFFFCSGNIEQPEDKFFNTPVEVLLFDNPQSDKEALQKGLAATLRYPRSPNGYLQIGSFYKGVAEG

Parental  EVDPAFGPLEALRLSIQTDSPVWVILSEIFLKKAD
          EV.PAFGPLEALRLSIQTDSPVWVILSE.FLKKAD
Retrocopy EVGPAFGPLEALRLSIQTDSPVWVILSESFLKKAD

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	0.02 RPM	14.47 RPM
SRP051959_heart	0.16 RPM	10.91 RPM
SRP051959_kidney	0.00 RPM	11.63 RPM
SRP051959_liver	0.02 RPM	9.90 RPM
SRP051959_lung	0.03 RPM	8.80 RPM
SRP051959_lymph_node	0.00 RPM	6.05 RPM
SRP051959_skeletal_muscle	0.02 RPM	8.63 RPM
SRP051959_spleen	0.00 RPM	6.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_508 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_508 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_508 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	ENSCJAG00000010124	1 retrocopy	retro_cjac_508 ,