RetrogeneDB ID: retro_cjac_1758

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:355988..356911(+)
• Located in intron of: ENSCJAG00000010221

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC10
• Ensembl ID: ENSCJAG00000021208
• Aliases: None
• Description: armadillo repeat containing 10 [Source:HGNC Symbol;Acc:21706]

Sequence

>retro_cjac_1758
ATAGGTGTCGCCTGGGGTGCAGGCTGGGTGGCGACAGTCCTGATCCTCGGCACGGACTCATGCTACTGCATTTACAGGCT
GACACACAGTCAGCGGCAGGGCAGCTGCGGGCTCAGTCTGCACTCCTCACAGTCCACGGAAGACTTAACTGATGGTTCAT
ATGATGATGCTCTGAATGCCGAACAACTTCAGAAACTCCTTTACCTGCTTGAGTCAACTGAGGATCCTATAATTATTGAA
AAAGCTTTGATTACTTTGGGTAACAATGCAGCCTTTTCAGTGAACCAAGCTATTATTCGTGAATTGGAGGGTATTCCAAT
TGCTGGAAACAAAATCAACCATTCCAACGAGAGTATTAAAGAGAAGCCTTTAAATGCACTTAACAACGGGAGTGTGAATG
TTGAAAATCAAATCAAGATAAAGATATACATCAGCCAAGTCTGTGAGGATGTCTTCTCTGGTCCTCTGAACTCTGCTGTG
CAGCTGGCTGGACTGAGATTGTTGACAAACATGACTGTTACCAATGACCACCAGCACATGCTTCACAGTTATATTACAGA
CCGGTTCCAGGTGTTACTTACTGGAAGTGGAAACATGAAGGTCCAAGTTTTGAAAATGCTTTTGAATTTGTCTGAAAATT
GAGCCATGACAGACGGACTTCTTCGTGCCCAAGTGGATGCGTCATTCTTTTCCCTTTATGACAGCCATGTAGCAAAGGAG
ATTCTTCTTTGAGTACTTACACTATTTCAGAATATGAATAACTGCCTCAAAATAGAAGGCCATTTAGCTGTGCAGCCACT
TTCACTGAAGGTTCATTGTTTTTCCTGTTATATGGAGAAGAATGTGCCCAGAAAGTAAGAGCTTTATTTCATCATGATGA
TGCAGAGGTGAAGGAAAAGATTGTAGCAATAATGTCCAAAATC

Alignment

ORF - retro_cjac_1758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGARGVGWVAAGLLLGAGACYCIYRLTRRRRRGDRGLVLRPSQSAEDLTDGSYDDVLNAEQLQKLLYLL
          .G.A.G.GWVA..L.LG...CYCIYRLT...R.G..GL.L..SQS.EDLTDGSYDD.LNAEQLQKLLYLL
Retrocopy IGVAWGAGWVATVLILGTDSCYCIYRLTHSQRQGSCGLSLHSSQSTEDLTDGSYDDALNAEQLQKLLYLL

Parental  ESTEDPIIIEKALITLGNNAAFSVNQAIIRELGGIPIVGNKINHSNQSIKEKALNALNNLSVNVENQIKI
          ESTEDPIIIEKALITLGNNAAFSVNQAIIREL.GIPI.GNKINHSN.SIKEK.LNALNN.SVNVENQIKI
Retrocopy ESTEDPIIIEKALITLGNNAAFSVNQAIIRELEGIPIAGNKINHSNESIKEKPLNALNNGSVNVENQIKI

Parental  KIYINQVCEDVFSGPLNSAVQLAGLRLLTNMTVTNDHQHMLHSYITDLFQVLLTGNGNTKVQVLKLLLNL
          KIYI.QVCEDVFSGPLNSAVQLAGLRLLTNMTVTNDHQHMLHSYITD.FQVLLTG.GN.KVQVLK.LLNL
Retrocopy KIYISQVCEDVFSGPLNSAVQLAGLRLLTNMTVTNDHQHMLHSYITDRFQVLLTGSGNMKVQVLKMLLNL

Parental  SENPAMTEGLLHAQVDASFLSLYDSHVAKEILLRVLTLFQNINNCLKIEGHLAVQP-TFTEGSLFFLLYG
          SEN.AMT.GLL.AQVDASF.SLYDSHVAKEILL.VLTLFQN.NNCLKIEGHLAVQP.TFTEGSLFFLLYG
Retrocopy SEN*AMTDGLLRAQVDASFFSLYDSHVAKEILL*VLTLFQNMNNCLKIEGHLAVQP<TFTEGSLFFLLYG

Parental  EECAQKIRALVDHDDAEVKEKVVTIMPKI
          EECAQK.RAL..HDDAEVKEK.V.IM.KI
Retrocopy EECAQKVRALFHHDDAEVKEKIVAIMSKI

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	0.49 RPM	8.72 RPM
SRP051959_heart	0.47 RPM	10.91 RPM
SRP051959_kidney	0.22 RPM	13.82 RPM
SRP051959_liver	0.11 RPM	7.08 RPM
SRP051959_lung	0.49 RPM	10.79 RPM
SRP051959_lymph_node	0.75 RPM	12.01 RPM
SRP051959_skeletal_muscle	0.15 RPM	4.28 RPM
SRP051959_spleen	0.65 RPM	11.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1758 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1758 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004247	1 retrocopy	retro_cfam_1264,
Choloepus hoffmanni	ENSCHOG00000002095	1 retrocopy	retro_chof_2665,
Callithrix jacchus	ENSCJAG00000021208	2 retrocopies	retro_cjac_1758 , retro_cjac_2104,
Cavia porcellus	ENSCPOG00000019936	1 retrocopy	retro_cpor_1022,
Homo sapiens	ENSG00000170632	1 retrocopy	retro_hsap_2815,
Microcebus murinus	ENSMICG00000010160	1 retrocopy	retro_mmur_638,
Myotis lucifugus	ENSMLUG00000006088	3 retrocopies	retro_mluc_1587, retro_mluc_1825, retro_mluc_624,
Mus musculus	ENSMUSG00000038525	3 retrocopies	retro_mmus_1292, retro_mmus_2256, retro_mmus_969,
Vicugna pacos	ENSVPAG00000008914	1 retrocopy	retro_vpac_19,