RetrogeneDB ID: retro_cjac_2191

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:145879602..145880319(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE1
• Ensembl ID: ENSCJAG00000020515
• Aliases: None
• Description: None

Sequence

>retro_cjac_2191
CTAGAGGAGTGGGACGTGAAGCGCATGCAGAAGCACTGCTAGAAGGTCCATGACCACAATGCCACCGTAGATAAGTTGGA
GGACTTCATCAAAAACATAAACAGTGTCTTGGAGTCCTTGTATATTGAGATAAAGAGAGGAGTCACGGAAGATAACGGGA
GACCCATTTATGCGCTGGTGAATCTTGCTACAACTTCAGTTTCCAAAATGGCTACGGATTTTGCAGAGAATGAGCTGGAT
CTGTTTAGAAAGGCCCTGGAACTGATCATCGACTCAGAAAGTGGCTTTGCATCTTCCACAAACATTTTGAACCTGGTTGA
TCAGCTTAAAGGAAAAAAGATGAAGAAGAAGGAAGCGGAGCTGGTGCTGCAGAAGTTTGTCCAAAACAAGTGGCTGATTG
AGAAGGAAGGGGAGTTCACCCTGCACGGCCGGGCCATCCTGGAGATGGAGTAGTACATCCGGGAGACGTACCCTGACTCA
GTGAAGATCTGCAATATCTGCCACAGCCTCCTCATCCAGGGTCAAAGCTGCAAGACCTGTGGAATCAGGATGCACTTACC
CTGCGTGGCCAAGTACTTCCGGTCGAATGCCAAACCGCGCTGCCCTCACTGCAACGACTACTGTCCCCATGAGATCCCAG
AAGTCTTCGACCCTGAGAAGGAGAGGGAGCCTGGTATCTCGAAATCGAACAAAAAGTCCCTGCGGTCCAGGCGGCAT

Alignment

ORF - retro_cjac_2191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 89.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEEWDVKRMQKHCYKVHDRNATVDKLEDFINNINSVLESLYIEIKRGVTEDDGRPIYALVNLATTSVSKM
          LEEWDVKRMQKHC.KVHD.NATVDKLEDFI.NINSVLESLYIEIKRGVTED.GRPIYALVNLATTSVSKM
Retrocopy LEEWDVKRMQKHC*KVHDHNATVDKLEDFIKNINSVLESLYIEIKRGVTEDNGRPIYALVNLATTSVSKM

Parental  ATDFAENELDLFRKALELIIDSESGFASSTNILNLVDQLKGKKMKKKEAELVLQKFVQNKWLIEKEVERS
          ATDFAENELDLFRKALELIIDSESGFASSTNILNLVDQLKGKKMKKKEAELVLQKFVQNKWLIEKE.E..
Retrocopy ATDFAENELDLFRKALELIIDSESGFASSTNILNLVDQLKGKKMKKKEAELVLQKFVQNKWLIEKEGEFT

Parental  LHPRVRVPSTQHNHCTQDGAVRICNICHSLLIQGQSCETCGIRMHLPCVAKYFRSNAEPRCPHCNDYWPH
          LH.R...........T....V.ICNICHSLLIQGQSC.TCGIRMHLPCVAKYFRSNA.PRCPHCNDY.PH
Retrocopy LHGRAILEME*YIRETYPDSVKICNICHSLLIQGQSCKTCGIRMHLPCVAKYFRSNAKPRCPHCNDYCPH

Parental  EIPEVFDPEKEREPGISKSNRKSLRSRRH
          EIPEVFDPEKEREPGISKSN.KSLRSRRH
Retrocopy EIPEVFDPEKEREPGISKSNKKSLRSRRH

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	0.73 RPM	3.39 RPM
SRP051959_heart	1.16 RPM	5.23 RPM
SRP051959_kidney	1.31 RPM	5.79 RPM
SRP051959_liver	2.08 RPM	9.27 RPM
SRP051959_lung	0.93 RPM	4.28 RPM
SRP051959_lymph_node	0.82 RPM	4.31 RPM
SRP051959_skeletal_muscle	1.35 RPM	6.16 RPM
SRP051959_spleen	1.32 RPM	3.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2191 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2191 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2191 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011003	2 retrocopies	retro_chof_1394, retro_chof_339,
Callithrix jacchus	ENSCJAG00000020515	1 retrocopy	retro_cjac_2191 ,
Dasypus novemcinctus	ENSDNOG00000013271	1 retrocopy	retro_dnov_641,
Mus musculus	ENSMUSG00000030750	2 retrocopies	retro_mmus_1564, retro_mmus_2488,
Ochotona princeps	ENSOPRG00000011452	1 retrocopy	retro_opri_732,