RetrogeneDB ID: retro_cjac_3980

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286460.1:124748..125324(-)
• 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_3980
TCCTTGTTTCTTAAAAAAAAACAGATCCCACTGGTCAGCCACGCCTACACCACTGCCTATGTCCTCATCACCCCAGCCGT
GCAATTGGAATTGATCACTGCTTTTCAGTTGTACTTCAATTCTGAATTAATCTTTAAACACTTTCAAATATTGAGATTAA
TCACCAATTTCTTATTTTTTGAGCCAGTTGGATTCAATTTTTTATTTAAGATGATTTTTCTATATTGTTACTGTCAAATG
CTAGAAGGCTCTTTCTGGGGTTGGACAGCAGACTTTGTATTTATATTCCTTTTTGGTGGATTCTTAATTACCCTTCTTAG
TTTGTTTTTGAGCTTAGTTTTCATGGGCCAGGCCTTTACAATAATGCTCGTCTACGTGTGGAGCCAAAGGAAACCCTATG
TCCACATGAATTTCTTCAGCCTTCTCAACTTCCAGGCCCCCTTTCTGCCCTGGGTGCACATGCGGTTTTCCCTGTTGGGG
AACTCAATCACTGTAGACCTTTTGGGTATTGCAGTAGGACACATATATTTTTTCATGGAAGATGTATTTTCTAATCAGCT
TGGTGGAATAAGAATA

Alignment

ORF - retro_cjac_3980 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.44 %
• Parental protein coverage: 81.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLRLEYLQIPPVSRAYTTACVLTTAAVQLELITPFQLYFNPELIFKHFQIWRLITNFLFFGPVGFNFLFN
          SL.L...QIP.VS.AYTTA.VL.T.AVQLELIT.FQLYFN.ELIFKHFQI.RLITNFLFF.PVGFNFLF.
Retrocopy SLFLKKKQIPLVSHAYTTAYVLITPAVQLELITAFQLYFNSELIFKHFQILRLITNFLFFEPVGFNFLFK

Parental  MIFLYRYCRMLEEGSFRGRTADFVFMFLFGGFLMTLFGLFVSLVFLGQAFTIMLVYVWSRRNPYVRMNFF
          MIFLY.YC.MLE.GSF.G.TADFVF.FLFGGFL.TL..LF.SLVF.GQAFTIMLVYVWS.R.PYV.MNFF
Retrocopy MIFLYCYCQMLE-GSFWGWTADFVFIFLFGGFLITLLSLFLSLVFMGQAFTIMLVYVWSQRKPYVHMNFF

Parental  GLLNFQAPFLPWVLMGFSLLLGNSIIVDLLGIAVGHIYFFLEDVFPNQPGGIRI
          .LLNFQAPFLPWV.M.FS.LLGNSI.VDLLGIAVGHIYFF.EDVF.NQ.GGIRI
Retrocopy SLLNFQAPFLPWVHMRFS-LLGNSITVDLLGIAVGHIYFFMEDVFSNQLGGIRI

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_3980 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3980 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,