RetrogeneDB ID: retro_cjac_2841

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:111345618..111346271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000034823
• Aliases: None
• Description: Glutathione S-transferase [Source:UniProtKB/TrEMBL;Acc:F7HBV1]

Sequence

>retro_cjac_2841
CTGGCAGCCAAACCCAAGCTCTACTGCTTTCACAGCAGGGGCAGGATGGAATCAGTCCACTGGCTGCTGGCTGCAGCTGG
AATGGAGTTTGAAGAATAATTTTTTTGAAATGAGAGAATAATGCGAAAAGTTGCAGAAGGATGATGCCTACTTTTTGGCC
AAGTGCCTTTGGTTGAAACTAATGTAATGATGCTGACACTGACTAGAGCCATGCTCGCTTCAGCTACCTTGCTAAGTACA
ATGTCTATGGGAAGGACCTGAAGGGGAGAGTGAGGATCAACATGTGTGCTGATGGTACCCTGGACCTGATGATGATGATG
GTGCTGGCCCCTGAGGAAAAGAGGAGAACCTTGCTTCGGTCATGATGAAAGCTGACACCTGGTACTTGCCCGTCTTTGGA
AAGATTTTGGAAGATCATAGAGCAGGTTTTCTCATTGGCAACAAATTCAGCTGGGCAGACATACAACTGTTAGAAGCTGT
TTTAATGGTAGAAGAACTCAAGCTTCTGTTCTTTTGGACTTCCCTCTGCTGAAGGCATTTAAAACAGGAATCAGCAACAT
CCCCACAATTAAGAAGTTCCTGCAACGTGGAGTCAGAGGAAGCTGTTCCCTGACATCCAGTATATTGATCTAGTTAGAAA
CATTCTATAGTTC

Alignment

ORF - retro_cjac_2841 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAAKPKLYYFHGRGRMESIRWLLAAAGVEFEE-EFLETREQYEKLQKDG-CLLFGQVPLVEVDGMM--LT
          .AAKPKLY.FH.RGRMES..WLLAAAG.EFEE..F.E.RE..EKLQKD..CLLFGQVPLVE...MM..LT
Retrocopy LAAKPKLYCFHSRGRMESVHWLLAAAGMEFEE>NFFEMRE*CEKLQKDD<CLLFGQVPLVETNVMMLTLT

Parental  Q-TRAILSYLAAKFNFYGKDLKERVRIDMYVDGTLDLMAMIMLAPFQRPEEK-QETLASVIQKAKARYFP
          ....A..SYLA.K.N.YGKDLK.RVRI.M..DGTLDLM.M..LA....PEEK..E.LASV..KA...Y.P
Retrocopy R<SHARFSYLA-KYNVYGKDLKGRVRINMCADGTLDLMMMMVLA----PEEK<EENLASVMMKADTWYLP

Parental  VFEKILKDHGEDFLVGNKFSWADIQMLEAILMVEEL-NASVLSDFPLLKAFKTRISNIPTIKKFLQPG-S
          VF.KIL.DH...FL.GNKFSWADIQ.LEA.LMVEEL..ASVL.DFPLLKAFKT.ISNIPTIKKFLQ.G.S
Retrocopy VFGKILEDHRAGFLIGNKFSWADIQLLEAVLMVEEL<QASVLLDFPLLKAFKTGISNIPTIKKFLQRG<S

Parental  QRKPPPDAHYVDLVSNILQF
          QRK..PD..Y.DLV.NIL.F
Retrocopy QRKLFPDIQYIDLVRNIL*F

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	0.07 RPM
SRP051959_heart	0.00 RPM	0.07 RPM
SRP051959_kidney	0.07 RPM	0.16 RPM
SRP051959_liver	0.00 RPM	1.28 RPM
SRP051959_lung	0.03 RPM	0.37 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2841 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2841 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2841 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2366
Pan troglodytes	retro_ptro_1732
Gorilla gorilla	retro_ggor_1797

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 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 ,
Otolemur garnettii	ENSOGAG00000031992	1 retrocopy	retro_ogar_2737,
Rattus norvegicus	ENSRNOG00000030449	1 retrocopy	retro_rnor_165,