RetrogeneDB ID: retro_cjac_1540

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:23947868..23948573(+)
• 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_1540
TACCAGAGCCTGCGGCTGGAGTACTTTCAGATCCCACCGGTCAGCCGCGCCTACACCACTGCTTGCATCCTCACCACCGC
AGCCCTGCAGTTGGAATTGATCACACCTTTTTAGTTGTACTTCAGTCCTCAATTTATCTTTAAACGCTTTCAAATATGGA
GATTAATCACCAATTTCTTATTTTGGGGGCCAGATGGATTCAATTTTTTAACATGATTTTTCCATATAGTTACTGTCAAA
TGCTAGAAGAAGGCTCTTTCCGAGGTCAGACAGGCGACTTTGTATTTATGTTCCTTTTTGGGGGATTCTTAATGACCCTT
TTTGGTTTGTTTGTGAGCTTAGTTTTCTTGGGCCAGGCCTGTACAATAATGCTCGTCTACGTGTGGTGCTGAAGGAACCC
CTATGTCTGTATGAACTTCTTCGGCCTTCTCAACTTCCAGGCTCCATTTCTGCCCTGAGTGCTCATGAGGTTTTCCTTGT
CAGGGAATTCAATCATTGTGGCTCTTTTGGGTATTGCAGTTGGACACATATATTTTTTTCTTGAAAGATGTATTTCCCAA
TCAGCCTAGTGGAATAAGAATTCTGAAAACACCACCTATCTTGAAAGCTATTTTTGATACAGCAGATGAGGATTCAAATT
ACAATCCACTACCTGAAGAACGGCCAGGAGGCTTCACCTGGGGTGAGGGCCAACGCCTCAAAGGT

Alignment

ORF - retro_cjac_1540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.1 %
• Parental protein coverage: 99.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YQSLRLEYLQIPPVSRAYTTACVLTTAAVQLELITPFQLYFNPELIFKHFQIWRLITNF-LFFGPVGFNF
          YQSLRLEY.QIPPVSRAYTTAC.LTTAA.QLELITPF.LYF.P..IFK.FQIWRLITNF.L..G.....F
Retrocopy YQSLRLEYFQIPPVSRAYTTACILTTAALQLELITPF*LYFSPQFIFKRFQIWRLITNF<LILGARWIQF

Parental  LFNMIFLYRYCRMLEEGSFRGRTADFVFMFLFGGFLMTLFGLFVSLVFLGQAFTIMLVYVWSRRNPYVRM
          .FNMIF.Y.YC.MLEEGSFRG.T.DFVFMFLFGGFLMTLFGLFVSLVFLGQA.TIMLVYVW..RNPYV.M
Retrocopy -FNMIFPYSYCQMLEEGSFRGQTGDFVFMFLFGGFLMTLFGLFVSLVFLGQACTIMLVYVWC*RNPYVCM

Parental  NFFGLLNFQAPFLPWVLMGFSLLLGNSIIVDLLGIAVGHIYFFLE-DVFPNQPGGIRILKTPSILKAIFD
          NFFGLLNFQAPFLP.VLM.FS.L.GNSIIV.LLGIAVGHIYFFLE.DVFPNQP.GIRILKTP.ILKAIFD
Retrocopy NFFGLLNFQAPFLP*VLMRFS-LSGNSIIVALLGIAVGHIYFFLE>DVFPNQPSGIRILKTPPILKAIFD

Parental  TPDEDPNYNPLPEERPGGFAWGEGQRLGG
          T.DED.NYNPLPEERPGGF.WGEGQRL.G
Retrocopy TADEDSNYNPLPEERPGGFTWGEGQRLKG

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	0.04 RPM	14.18 RPM
SRP051959_heart	0.00 RPM	8.54 RPM
SRP051959_kidney	0.00 RPM	14.18 RPM
SRP051959_liver	0.02 RPM	23.72 RPM
SRP051959_lung	0.23 RPM	12.49 RPM
SRP051959_lymph_node	0.50 RPM	14.59 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.65 RPM
SRP051959_spleen	0.15 RPM	18.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1540 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1540 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,