RetrogeneDB ID: retro_cjac_2104

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:20490970..20491893(-)
• Located in intron of: ENSCJAG00000000762

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_2104
ATGGGTGGCACCTGGGGCACAGGCTGGGTCGAGACAGGCCTGCTCCTCAGCACGGATGCATGCTACTGCATTTACAGGCT
GACACGCAGTCAGCGGCAGGGCAGCCGTGGGCTCAGTCTGCGCTCCTCACAGTCCACAGAAGACTTAACTGATGGTTCAT
ATGATGATGTTCTGAATGCCGAATAACTTCAGAAACTCCTTTACCTGCTTGAGTCAACTGAGGATCCTATAATTATTGAA
AAAGCTTTGATTACTTTGGGTAACAATGCAGCCTTTTCAGTGAACCAAGCTATTATTCATGAATTGGAGGGTATTCCAAT
TGCTGGAAACAAAATCAACCATTCCAACCAGAGTATTAAAGAGAAGGCTTTAAATGCACTTAACAACGGGAGTGTGAATG
TTGAAAATCAAATCAAGATAAGGATATACATCAGCCAAGTCTGTGAGGATGTCTTCTCTGGTCCTCTGAACTCTGCTGTG
CAGCTGGCCAGACTGAGATTGTTGACAAACATGACTGTTACCAATGACCACCAGCACATGCTTCACAGTTATATTACAGA
CCGGTCCCAGGTGTTACTTACTGGAAGTGGAAACACGAAAGTCCAAGTTTTGAAACTGCTTTTGAATTTGTCTGAAAATC
CAGCCATGACAGACGGACTTCTCTGTGCCCAAGTGGATACGTCATTCTTTTTCCTTTATGGCAGCCATGTAGCAAAGGAG
ATTCTTCTTCAAGTACTTACACTATTTCAGAATATGAATAACTGCCTCAAAATAGAAGGCCATTTAGCTGTGCAGCCACT
TTCACTGAAGGTTCATTGTTTTTCCTGTTATATGGAGAAGAATGTGCCCAGAAAGTAAGAGCTTTATTTCATCATGATGA
TGCAGAGGTGAAGGAAAAGGTTGTAACAATAATGCCCAAAATC

Alignment

ORF - retro_cjac_2104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGARGVGWVAAGLLLGAGACYCIYRLTRRRRRGDRGLVLRPSQSAEDLTDGSYDDVLNAEQLQKLLYLL
          MGG..G.GWV..GLLL...ACYCIYRLTR..R.G.RGL.LR.SQS.EDLTDGSYDDVLNAE.LQKLLYLL
Retrocopy MGGTWGTGWVETGLLLSTDACYCIYRLTRSQRQGSRGLSLRSSQSTEDLTDGSYDDVLNAE*LQKLLYLL

Parental  ESTEDPIIIEKALITLGNNAAFSVNQAIIRELGGIPIVGNKINHSNQSIKEKALNALNNLSVNVENQIKI
          ESTEDPIIIEKALITLGNNAAFSVNQAII.EL.GIPI.GNKINHSNQSIKEKALNALNN.SVNVENQIKI
Retrocopy ESTEDPIIIEKALITLGNNAAFSVNQAIIHELEGIPIAGNKINHSNQSIKEKALNALNNGSVNVENQIKI

Parental  KIYINQVCEDVFSGPLNSAVQLAGLRLLTNMTVTNDHQHMLHSYITDLFQVLLTGNGNTKVQVLKLLLNL
          .IYI.QVCEDVFSGPLNSAVQLA.LRLLTNMTVTNDHQHMLHSYITD..QVLLTG.GNTKVQVLKLLLNL
Retrocopy RIYISQVCEDVFSGPLNSAVQLARLRLLTNMTVTNDHQHMLHSYITDRSQVLLTGSGNTKVQVLKLLLNL

Parental  SENPAMTEGLLHAQVDASFLSLYDSHVAKEILLRVLTLFQNINNCLKIEGHLAVQP-TFTEGSLFFLLYG
          SENPAMT.GLL.AQVD.SF..LY.SHVAKEILL.VLTLFQN.NNCLKIEGHLAVQP.TFTEGSLFFLLYG
Retrocopy SENPAMTDGLLCAQVDTSFFFLYGSHVAKEILLQVLTLFQNMNNCLKIEGHLAVQP<TFTEGSLFFLLYG

Parental  EECAQKIRALVDHDDAEVKEKVVTIMPKI
          EECAQK.RAL..HDDAEVKEKVVTIMPKI
Retrocopy EECAQKVRALFHHDDAEVKEKVVTIMPKI

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	8.72 RPM
SRP051959_heart	0.11 RPM	10.91 RPM
SRP051959_kidney	0.07 RPM	13.82 RPM
SRP051959_liver	0.00 RPM	7.08 RPM
SRP051959_lung	0.03 RPM	10.79 RPM
SRP051959_lymph_node	0.02 RPM	12.01 RPM
SRP051959_skeletal_muscle	0.02 RPM	4.28 RPM
SRP051959_spleen	0.06 RPM	11.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2104 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2104 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,