RetrogeneDB ID: retro_cjac_3886

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285818.1:49130..49673(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DERL2
• Ensembl ID: ENSCJAG00000011304
• Aliases: LOC100400027, DERL2, derlin-2
• Description: derlin 2 [Source:HGNC Symbol;Acc:17943]

Sequence

>retro_cjac_3886
TCAGCTGTGCCTACACCACTGCCCATGCACTTGGAATTGATCACTGCTTTTCAGTTGTACTTCAATCCTGAATTAATCTT
TAAACACTTTAAAATATTGAGATTAATCACCAATTTCTTATTTTTTGAGCCAGTTGGATTCAATTTTTTATTTAACATGA
TTTTTCTATATTGTTACTGTCCAATGCTAGAAGGCTCTTTCTGGGGTTGGACAGCAAACTTGGTATTTATATTCCTTTTT
GGTGGATTCTTAATGACCCTTCTTAGTTTGTTTTTGAGCTTAGTTTTCATGGGCCAGGCCTTTACAATAATGCTCGTCTA
TGTGTGGAGCCAAAGGAAATCCTATGTCCACATGAACTTCTTCAGCCTTCTCAACTTCCAGGCCCCCTTTCTGCCCTGGG
TGTTCATGGGGTTTTCCTTGTTGGGGAACTCAATCACTGTAGACCTTTTGGGTATTGCAGTTGGACACATATATTTTTTC
TTGGAAGATGTATTTTCTAATTAGCTTGATGGAATAAGAATTCTGAAACCACCATCTATCTTG

Alignment

ORF - retro_cjac_3886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.78 %
• Parental protein coverage: 76.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ACVLTTAAVQLELITPFQLYFNPELIFKHFQIWRLITNFLFFGPVGFNFLFNMIFLYRYCRMLEEGSFRG
          ..V.T.....LELIT.FQLYFNPELIFKHF.I.RLITNFLFF.PVGFNFLFNMIFLY.YC.MLE.GSF.G
Retrocopy SAVPTPLPMHLELITAFQLYFNPELIFKHFKILRLITNFLFFEPVGFNFLFNMIFLYCYCPMLE-GSFWG

Parental  RTADFVFMFLFGGFLMTLFGLFVSLVFLGQAFTIMLVYVWSRRNPYVRMNFFGLLNFQAPFLPWVLMGFS
          .TA..VF.FLFGGFLMTL..LF.SLVF.GQAFTIMLVYVWS.R..YV.MNFF.LLNFQAPFLPWV.MGFS
Retrocopy WTANLVFIFLFGGFLMTLLSLFLSLVFMGQAFTIMLVYVWSQRKSYVHMNFFSLLNFQAPFLPWVFMGFS

Parental  LLLGNSIIVDLLGIAVGHIYFFLEDVFPNQPGGIRILKTPSIL
          .LLGNSI.VDLLGIAVGHIYFFLEDVF.N...GIRILK.PSIL
Retrocopy -LLGNSITVDLLGIAVGHIYFFLEDVFSN*LDGIRILKPPSIL

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	14.18 RPM
SRP051959_heart	0.00 RPM	8.54 RPM
SRP051959_kidney	0.00 RPM	14.18 RPM
SRP051959_liver	0.00 RPM	23.72 RPM
SRP051959_lung	0.00 RPM	12.49 RPM
SRP051959_lymph_node	0.00 RPM	14.59 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.65 RPM
SRP051959_spleen	0.00 RPM	18.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3886 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3886 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011304	3 retrocopies	retro_cjac_1540, retro_cjac_3886 , retro_cjac_3980,
Oryctolagus cuniculus	ENSOCUG00000004811	2 retrocopies	retro_ocun_1561, retro_ocun_1908,
Tupaia belangeri	ENSTBEG00000009213	1 retrocopy	retro_tbel_2788,
Tarsius syrichta	ENSTSYG00000000394	4 retrocopies	retro_tsyr_1148, retro_tsyr_1538, retro_tsyr_2049, retro_tsyr_537,