RetrogeneDB ID: retro_cjac_4055

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:40253688..40254346(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011287
• Aliases: None
• Description: Glutathione S-transferase [Source:UniProtKB/TrEMBL;Acc:F7FH40]

Sequence

>retro_cjac_4055
ATGGCGGGAAAGCCAAGCTTCACTCCTTCAATGCATGGGGCAGAATAGAGCCCATCCAGTGCTCTTGGCTGCAGCTGGAG
TGGAGTTTGAAGAGAAATTTCTAGAATCTGCAGAAGATTTGGAAACGTTAAGAAATGATGGGTATTTGCTGTTCCAGCAA
GTGCCAATGGTTGAGATTGACGGGATGAAGCTGGTGCAGATGAGAGCCATTCTCAACTACATTGCCAGCAAATACGACCT
CTATGGGAAAGACGTAAAGGAGAGAGCCCTGATTGATATGTATACAGGAGGTATGGCAGGTTTGTATGAAATGATCCTTC
TGCCCTTATGCCGACCTGAGGAAAAAGATGCCAAGATTGCCTTGATCCAAGAGAAAACAAAAAATCGCTATTTCCCTGCC
TTCGAAATAGTGTTAAAGAGCCACAAACAAGACTACCTTGTTGGCAACAAGCTGAGCTGGGCTGACATTCAGCTGGTGGA
ACTTCTCTACTTTGTGGAAGAGCTTGACCCCAGCCTTATCTCCAGCTTCCTTCTGCTGTAGGCCCTGAAAACCAGAATCA
GCAACCTGACCACGGTGAAGAAGTTTCTGCAACCTGGCAGCCCAAGGAAGCCTCTTACAAATGCGAAATCTGTAGAAGAA
GCAAGGAAGATTTTCAAG

Alignment

ORF - retro_cjac_4055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.24 %
• Parental protein coverage: 99.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGKP-KLHYFNARGRMEPIRW-LLAAAGVEFEEQFLESAEDLEKLKNDGYLMFQQVPMVEIDGMKLVQS
          MAGKP.KLH.FNA.GR.EPI...LLAAAGVEFEE.FLESAEDLE.L.NDGYL.FQQVPMVEIDGMKLVQ.
Retrocopy MAGKP<KLHSFNAWGRIEPIQC<LLAAAGVEFEEKFLESAEDLETLRNDGYLLFQQVPMVEIDGMKLVQM

Parental  RAILNYIASKYDLYGKDLKERALIDMYTEGMADLYEMILLLPLCRPEEKDTKIALIQEKTKNRYFPAFEK
          RAILNYIASKYDLYGKD.KERALIDMYT.GMA.LYEMILL.PLCRPEEKD.KIALIQEKTKNRYFPAFE.
Retrocopy RAILNYIASKYDLYGKDVKERALIDMYTGGMAGLYEMILL-PLCRPEEKDAKIALIQEKTKNRYFPAFEI

Parental  VLKSHEQDYLVGNKLSRADIQLVELLYFVEELDPSLISSFPLLQALKTRISNLPTVKKFLQPGSPRKPPT
          VLKSH.QDYLVGNKLS.ADIQLVELLYFVEELDPSLISSF.LL.ALKTRISNL.TVKKFLQPGSPRKP.T
Retrocopy VLKSHKQDYLVGNKLSWADIQLVELLYFVEELDPSLISSFLLL*ALKTRISNLTTVKKFLQPGSPRKPLT

Parental  NAKSVEEARKIFK
          NAKSVEEARKIFK
Retrocopy NAKSVEEARKIFK

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	2.15 RPM
SRP051959_heart	0.04 RPM	1.19 RPM
SRP051959_kidney	0.00 RPM	312.56 RPM
SRP051959_liver	0.02 RPM	1219.71 RPM
SRP051959_lung	0.03 RPM	0.91 RPM
SRP051959_lymph_node	0.00 RPM	0.50 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.07 RPM
SRP051959_spleen	0.02 RPM	0.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4055 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4055 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011287	1 retrocopy	retro_cjac_4055 ,
Callithrix jacchus	ENSCJAG00000034823	2 retrocopies	retro_cjac_2783, retro_cjac_2841,
Dasypus novemcinctus	ENSDNOG00000009819	1 retrocopy	retro_dnov_2390,
Microcebus murinus	ENSMICG00000002208	1 retrocopy	retro_mmur_350,
Otolemur garnettii	ENSOGAG00000003726	1 retrocopy	retro_ogar_345,
Tupaia belangeri	ENSTBEG00000001413	1 retrocopy	retro_tbel_2120,