RetrogeneDB ID: retro_cjac_363

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:72984095..72985184(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021963
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TDP2
• Ensembl ID: ENSCJAG00000006074
• Aliases: None
• Description: None

Sequence

>retro_cjac_363
ATGGAGCTCGGCGGCTGCCTGGAGAGCGGGACAGAGGCGGCGGGGGAAGAGGGCGAGCCCGCGGTGAAGAAGCGGCGACT
TCTGTGTTTGGAGTTTGCCTCGGTCGCGAACTGCGATTCCGCTGTGGCTCAGTGCTACCTGGCCGAGAACGACTGGGAGA
TGGAAAGGGCACTGAACTCCTACTTCGAGCCTCCGGTGGAGGAGAGCGCCTTGGAACGCGGTCCTGAAACCACCGCCGAG
CCCAGGATCTATGTTGACCTAACCAATGAAGACACAACGGATTCTACCAGTTCTAAAATCAGCCCATCTGAAGATACTCA
GCAAGAAAATGGCAGCATGTTCTCTCTCATGACCTGGAATGTTGATGGATTAGATCTAAACAATCTGGCAGAGAGGGCTC
GAGGGGTGTGTTCCTATTTAGTTTTGTACAGCCCAGATGTGGTCTTCCTACAGGAAGTTATTCCCCCATATTGTAGCTAC
CTAAAGAAGAGAGCAAAAAATTATGAGATTATTACAGGTCATGAAGAAGGATATTTCACAGCTATAATGTTGAAGAAATC
AAGAGTGAAATTAAAAAGCCAAGAGATTATTCCTTTTCCAAGTACCAATATGATGAGAAACCTTTTGTGTGTGCATGTGA
ATGTGTCAGGAAATGAGCTTTGTCTTATGACATCCCATTTGGAGAGCACCAAAGGGCATGCTAAGGAACGAATGAATCAG
TTAAAAATAGTTTTAAAGAAAATGCAAGAGGCTCCAGAGTCAGCAACAGTTATATTTGCAGGAGATACAAATCTAAGGGA
TCAAGAGATTACCAAATGTGGTGGTTTACCCAGCAACATCGTGGATGTCTGGGAGTTGTTGGGCAAACCTAAACATTGCC
AGTATACATGGGATACACAGATGAACTCTAATCTTGGAATAACTGCTGCTTGTAAGCTTCGTTTTGATCGAATATTTTTC
AGAGCAGCAGCAGAAGAGGGACACATTATTCCCCGAAGTTTGGACCTTCTTGGATTGGAAAAACTGGACTGTGGTAGATT
TCCTAGTGATCACTGGGGTCTTCTGTGCAACTTAGATATAATACTGTAA

Alignment

ORF - retro_cjac_363 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELGGCLEGGTEAAGEEGEPAVKKRRLLCLEFASVANCDSAVAQCYLAENDWEMERALNSYFEPPVEESA
          MELGGCLE.GTEAAGEEGEPAVKKRRLLCLEFASVANCDSAVAQCYLAENDWEMERALNSYFEPPVEESA
Retrocopy MELGGCLESGTEAAGEEGEPAVKKRRLLCLEFASVANCDSAVAQCYLAENDWEMERALNSYFEPPVEESA

Parental  LERRPETTAEPRIYVDLTNEETTDSTSSKISPSEDTQQENGSMFSLMTWNVDGLDLNNLAERARGVCSYL
          LER.PETTAEPRIYVDLTNE.TTDSTSSKISPSEDTQQENGSMFSLMTWNVDGLDLNNLAERARGVCSYL
Retrocopy LERGPETTAEPRIYVDLTNEDTTDSTSSKISPSEDTQQENGSMFSLMTWNVDGLDLNNLAERARGVCSYL

Parental  VLYSPDVVFLQEVIPPYCSYLKKRAKNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTNMMRNLLC
          VLYSPDVVFLQEVIPPYCSYLKKRAKNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTNMMRNLLC
Retrocopy VLYSPDVVFLQEVIPPYCSYLKKRAKNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTNMMRNLLC

Parental  VHVNVSGNELCLMTSHLESTKGHAKERMNQLKIVLKKMQEAPESATVIFAGDTNLRDQEVTKCGGLPSNI
          VHVNVSGNELCLMTSHLESTKGHAKERMNQLKIVLKKMQEAPESATVIFAGDTNLRDQE.TKCGGLPSNI
Retrocopy VHVNVSGNELCLMTSHLESTKGHAKERMNQLKIVLKKMQEAPESATVIFAGDTNLRDQEITKCGGLPSNI

Parental  VDVWELLGKPKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAAEEGHIIPRSLDLLGLEKLDCGRFPSD
          VDVWELLGKPKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAAEEGHIIPRSLDLLGLEKLDCGRFPSD
Retrocopy VDVWELLGKPKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAAEEGHIIPRSLDLLGLEKLDCGRFPSD

Parental  HWGLLCNLDIIL
          HWGLLCNLDIIL
Retrocopy HWGLLCNLDIIL

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	0.62 RPM	9.34 RPM
SRP051959_heart	0.32 RPM	4.58 RPM
SRP051959_kidney	0.89 RPM	11.91 RPM
SRP051959_liver	0.56 RPM	8.79 RPM
SRP051959_lung	0.57 RPM	10.15 RPM
SRP051959_lymph_node	0.30 RPM	9.38 RPM
SRP051959_skeletal_muscle	0.44 RPM	3.41 RPM
SRP051959_spleen	0.38 RPM	10.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_363 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_363 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_363 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012012	2 retrocopies	retro_chof_2007, retro_chof_616,
Callithrix jacchus	ENSCJAG00000006074	1 retrocopy	retro_cjac_363 ,
Dasypus novemcinctus	ENSDNOG00000010113	1 retrocopy	retro_dnov_500,
Ochotona princeps	ENSOPRG00000016299	2 retrocopies	retro_opri_261, retro_opri_939,