RetrogeneDB ID: retro_cjac_2494

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:209984..210890(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLIN2
• Ensembl ID: ENSCJAG00000008088
• Aliases: None
• Description: None

Sequence

>retro_cjac_2494
ATGGCATCCTTTGCAGTTGATCCACAACCCAGTGTCATGACTCGGGTGGTCAACCTGCCGTTGGTGAGCTCCACATATGA
CCTCATGTCCTCAGCCTATGTCAATACAAAGGACCAGTATCCCTACTTGAAGTCTGTGTGTGAGATGGCAGAGAAGGGTG
TGAAGACCATCACCTCTGTGGCCCTGACCAGTGATCTGCCCATCATCCAGAAGCTAGAGCCACAAATTGCAATTGCCAAT
ACCTATGCCTGTAAGGGCCTAGACAGGATGGAGGAGAGACTGCCTATTCTGAATCAGCCATCAACTCAGGTTGTTGCCAA
TGCCAAAGGTGCTGTGACTGGGCCAAAAGATGCTGTGACAACTACTAGGACTGGGACCAAGGATTCCGTGGCCAGCACAA
TCACAAGGGTGATGGACAAGACCAAAAGGGCAGTGACTGGCAGTGTGGAGAAGACCAAGTCTGTGGTCAGTGGCAGCATT
AACAGTCTTGGGGAGTTGGATGATGCAGCTCGTGAGCAGTGGTGTAGAAAATGCACTCACCAAATCAGAGCTGTTGGTAG
AACAGTACCTCCCTCTCACAAAGAAGAGCTAGGAAAAGAAGCAAAAAAACTTGAAGGATTTGATATGGTTCAGAAGCCAA
GTTATTATGTTAGACTGGGATCCCTGTCTACCAAGCTTCGCTCCCGCACCTACTAGCACGCTCTCAGCAGGGTTAAAGAA
GCTAAGCAAAAAAGCCAAGAGACCATTTCTCAGCTCCATTCTACTGTTCACCTGATTGAATCTGCCAGGAAGAATGTGCA
TAGTGCCAATCAGAAAATTCAGGACGCTCAGGATGAACTCTACCTCTCATGGGTGGAGTGGAGAAGGAGCATTGGATATG
ATGATACTGATGAGTCCCACTGTGCT

Alignment

ORF - retro_cjac_2494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.49 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASVAVDPQPSVVTRVVNLPLVSSTYGLMSSAYVNTKDQYPYLKSVCEMAEKGVKTITSVALTSALPIIQ
          MAS.AVDPQPSV.TRVVNLPLVSSTY.LMSSAYVNTKDQYPYLKSVCEMAEKGVKTITSVALTS.LPIIQ
Retrocopy MASFAVDPQPSVMTRVVNLPLVSSTYDLMSSAYVNTKDQYPYLKSVCEMAEKGVKTITSVALTSDLPIIQ

Parental  KLEPQIAVANTYACKGLDRMEERLPILNQPSTQVVANAKGAMTGAKDAVTTTVTGAKDSVASTITGVMDK
          KLEPQIA.ANTYACKGLDRMEERLPILNQPSTQVVANAKGA.TG.KDAVTTT.TG.KDSVASTIT.VMDK
Retrocopy KLEPQIAIANTYACKGLDRMEERLPILNQPSTQVVANAKGAVTGPKDAVTTTRTGTKDSVASTITRVMDK

Parental  TKGAVTGSVEKTKSVVSGSINTVLG-SRMMQLVSSGVENALTKSELLVEQYLPLT-EEELEKEAKKVEGF
          TK.AVTGSVEKTKSVVSGSIN..LG.S.MMQLVSSGVENALTKSELLVEQYLPLT..EEL.KEAKK.EGF
Retrocopy TKRAVTGSVEKTKSVVSGSINS-LG>SWMMQLVSSGVENALTKSELLVEQYLPLT<KEELGKEAKKLEGF

Parental  DMVQKPSYYVRLGSLSTKLRSRAYQQALSRVKEAKQKSQETISQLHSTVQLIEFARKNVHNTNQRIQDAQ
          DMVQKPSYYVRLGSLSTKLRSR.Y..ALSRVKEAKQKSQETISQLHSTV.LIE.ARKNVH..NQ.IQDAQ
Retrocopy DMVQKPSYYVRLGSLSTKLRSRTY*HALSRVKEAKQKSQETISQLHSTVHLIESARKNVHSANQKIQDAQ

Parental  DKLYLSWVEWKRSIGYDDTDESHCA
          D.LYLSWVEW.RSIGYDDTDESHCA
Retrocopy DELYLSWVEWRRSIGYDDTDESHCA

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	0.07 RPM	7.08 RPM
SRP051959_heart	0.04 RPM	10.28 RPM
SRP051959_kidney	0.09 RPM	60.90 RPM
SRP051959_liver	0.02 RPM	9.18 RPM
SRP051959_lung	0.07 RPM	7.26 RPM
SRP051959_lymph_node	0.07 RPM	5.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.44 RPM
SRP051959_spleen	0.06 RPM	9.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2494 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2494 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002827	1 retrocopy	retro_amel_321,
Callithrix jacchus	ENSCJAG00000008088	1 retrocopy	retro_cjac_2494 ,
Latimeria chalumnae	ENSLACG00000017943	1 retrocopy	retro_lcha_61,