RetrogeneDB ID: retro_cjac_4217

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:116637032..116638109(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF577
• Ensembl ID: ENSCJAG00000002084
• Aliases: None
• Description: None

Sequence

>retro_cjac_4217
GGGTCATTGTCATTAGAAGACGTGGCTGTGGACTTCACCAGAGAGGAGTGGTAGTTTCTGGACTCATCTTAGAAGGTCTT
GTACAAGGAAGTAATGTTGGAGAACTACAGAAACCTAGTATCAGTAGGGTATCAAGGCACCAAGCCAGATTCACTCTTCA
AGTTGGAGCAGGAGAACCCCCATGGATAGGAGAAGGAGTGGCCCACAGTCAAACCTGTCCGGGTTTTGTGATCCAGAATA
GAAGATATGTAGGAAAAGATTCTGATGCATTTGGTGGATATGGGAAATCATGCCTCCATATCAAACATGACAAAACCCTT
ACTGGAATTAAATACCATAGATGTGTTAAACCCTGTAGCACTAAATCACAGCTCAGTGACCATCAAAAAATGTATGCAGA
AAAGAAACCACATGAATACAGTGTGTGCAGGAGAGCCTTCTCCAGGAGAGCATAGCTTATTCAACATCAGAGAACTGAGA
GAGGAGAGAAACCCCATGGATGTGGTGAATGTGGGAAAACATTTATGAGGAAGATTTAGCTCACTGAGCATCAGAGAACT
CATATGGGAGAGAGACCCCACGAATGTAGTGAATGTGGAAAAGCCTTCTCCAGAAAGTCACAGCTCATGGTCCATCAGAA
GACCCATGTAGGAGAGAAACCCTATGGATGCAGTGAATGCGTAAAAGCCTTCAGCTGGAAGTGCCTGCTCAATAGACATC
AGCGATCCCATACTTAGAGAGAAACTCTGTGGGTGCAGTGTGTGTGGGAAAGCCTTTTCCCAGAAGGCATACCTCCTTGC
ACACTAGAGACTTCACACAGGAGAGAAGCCTTACGAATGCAGTGATTGTGGAACAACCTTCTATTTTAAGTTAGACCTGA
CCGGACATCAGCAGATTCATACAGGAGAGAAACCTTATGAATGTAGTGAGTGTGAAAAAGCCTTTAGAAGAAAGTCAAAG
CTCATTCAGCATCAACGTACTCATACCGGAGAGAGACTGTATTCCTGCAGCAAGTGTGGCAAAGCTTTTGCCCACGTCAG
TCCTCATTAAACATAAGAAAACTCACATAAGAGAGAA

Alignment

ORF - retro_cjac_4217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.66 %
• Parental protein coverage: 74.58 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLLSFEDVAVDFTREEWQFLDPSQKVLYKEVMSENYRNLVSVGYQGTKPDSLFKLER-GKPPWI-EGAAH
          G.LS.EDVAVDFTREEW.FLD.S.KVLYKEVM.ENYRNLVSVGYQGTKPDSLFKLE..G.PPWI.EG.AH
Retrocopy GSLSLEDVAVDFTREEW*FLDSS*KVLYKEVMLENYRNLVSVGYQGTKPDSLFKLEQ<GEPPWIGEGVAH

Parental  SETCPGFVIQNTRDAGKDSDAFGGYGKSCLHIKHDKTLTGIKYHRCVKASSTKSQLSDHPKIYAGEKLHE
          S.TCPGFVIQN.R..GKDSDAFGGYGKSCLHIKHDKTLTGIKYHRCVK..STKSQLSDH.K.YA..K.HE
Retrocopy SQTCPGFVIQNRRYVGKDSDAFGGYGKSCLHIKHDKTLTGIKYHRCVKPCSTKSQLSDHQKMYAEKKPHE

Parental  CSVCGRVFSRKAQLIQHQRTERGEKPHGCGECGKTFMRKIQLTEHQRTHTGEKPHECRECGKAFSRKSQL
          .SVC.R.FSR.A.LIQHQRTERGEKPHGCGECGKTFMRKI.LTEHQRTH.GE.PHEC.ECGKAFSRKSQL
Retrocopy YSVCRRAFSRRA*LIQHQRTERGEKPHGCGECGKTFMRKI*LTEHQRTHMGERPHECSECGKAFSRKSQL

Parental  TVHQKTHTGEKPYRCSECGKAFSRKCLLNRHQRSHT-GEKLFGCSVCGKAFSQKAYLIAHQRLHTGEKPY
          .VHQKTH.GEKPY.CSEC.KAFS.KCLLNRHQRSHT..EKL.GCSVCGKAFSQKAYL.AH.RLHTGEKPY
Retrocopy MVHQKTHVGEKPYGCSECVKAFSWKCLLNRHQRSHT>REKLCGCSVCGKAFSQKAYLLAH*RLHTGEKPY

Parental  ECSDCGRSFYFKSDLTRHQRIHTGEKPYECSECEKAFRSKSKLIQHQRTHTGERPYSCSDCGKAFAHMSV
          ECSDCG..FYFK.DLT.HQ.IHTGEKPYECSECEKAFR.KSKLIQHQRTHTGER.YSCS.CGKAFAH.S.
Retrocopy ECSDCGTTFYFKLDLTGHQQIHTGEKPYECSECEKAFRRKSKLIQHQRTHTGERLYSCSKCGKAFAHVSP

Parental  LIKHKKTHIRE
          .......H.RE
Retrocopy H*T*ENSHKRE

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	1.71 RPM
SRP051959_heart	0.00 RPM	3.70 RPM
SRP051959_kidney	0.00 RPM	3.90 RPM
SRP051959_liver	0.00 RPM	1.13 RPM
SRP051959_lung	0.00 RPM	3.46 RPM
SRP051959_lymph_node	0.00 RPM	3.84 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.64 RPM
SRP051959_spleen	0.00 RPM	4.41 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4217 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4217 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002084	1 retrocopy	retro_cjac_4217 ,