RetrogeneDB ID: retro_cjac_682

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:44333816..44334412(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MIS18A
• Ensembl ID: ENSCJAG00000009090
• Aliases: None
• Description: MIS18 kinetochore protein homolog A (S. pombe) [Source:HGNC Symbol;Acc:1286]

Sequence

>retro_cjac_682
GAGTAGGGTGACAAGGGCAAGTGCAGTGACTCCTTGCTGTTGAGCAAGAGGCTCTCTGAAGACTCAAGCTGCCACCAGGT
GCTGCAGAAGTCGACGAATATGTGGCGCTCCACAAGTGAGGACGCGTCGGTGGCCAACAAGGAGAAGGCGCGGCTCGAGG
AGGTGGAGGCGGCAGAGGAGAGGCTGCTGGTGTTCCTGTGCTCCAGCTGCTGGCGGCCGCTGGGTGACTCGCGAGCTGGG
TGACCAGCCAAAAGGACACCAACTGTATCCTGCTGCACTGTGTTTCCTGTAATGTTTCTGTGGGTAAGGAACAGAAGTTA
TCCACATGTGAAAAGGAAAATGGTTGCATCCTTGAAACTTTGTACTGCACGGGGTGCTCACTCAACCTTGGCTACGTGTA
TAGATGCACACCCAAGAATCTTGATTACAAGAGAGACTTGTTTTGCCTCAGTATTGAAGCCATCAAAAGCTATGTTTTAG
GGTCCTCTGAAAAGCAAATTGTGTCAGAAGATAAAGAACTTTTTAATCTTGAAAGCCGTGTTGAAATAGAAAAGTCTCTA
AAACAGATGGAAGATGTCTTGCAAAAGTACAGATTG

Alignment

ORF - retro_cjac_682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88. %
• Parental protein coverage: 85.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYGDKGKCSDSSLLSKRLSEDSSRHQLLQKWTNMWRSTSEDASVADTEKARLEEAAAAEERPLVFLCSSC
          E.GDKGKCSDS.LLSKRLSEDSS.HQ.LQK.TNMWRSTSEDASVA..EKARLEE..AAEER.LVFLCSSC
Retrocopy E*GDKGKCSDSLLLSKRLSEDSSCHQVLQKSTNMWRSTSEDASVANKEKARLEEVEAAEERLLVFLCSSC

Parental  RRPLGDS-LSWVTSQEDTNCILLRCVSCNVSVDKEQKLSKREKENGCILETLYCTGCSLNLGYVYRCTPK
          .RPLGDS..SWVTSQ.DTNCILL.CVSCNVSV.KEQKLS..EKENGCILETLYCTGCSLNLGYVYRCTPK
Retrocopy WRPLGDS<ASWVTSQKDTNCILLHCVSCNVSVGKEQKLSTCEKENGCILETLYCTGCSLNLGYVYRCTPK

Parental  NLDYKRDLFCLSVEAIESYVLGSSEKQIVSEDKELFNLESRVEIEKSLKQMEDVLQALQM
          NLDYKRDLFCLS.EAI.SYVLGSSEKQIVSEDKELFNLESRVEIEKSLKQMEDVLQ....
Retrocopy NLDYKRDLFCLSIEAIKSYVLGSSEKQIVSEDKELFNLESRVEIEKSLKQMEDVLQKYRL

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	1.18 RPM
SRP051959_heart	0.00 RPM	1.44 RPM
SRP051959_kidney	0.00 RPM	1.02 RPM
SRP051959_liver	0.00 RPM	0.56 RPM
SRP051959_lung	0.00 RPM	1.90 RPM
SRP051959_lymph_node	0.00 RPM	1.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.50 RPM
SRP051959_spleen	0.00 RPM	2.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_682 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_682 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009090	1 retrocopy	retro_cjac_682 ,
Ictidomys tridecemlineatus	ENSSTOG00000004511	1 retrocopy	retro_itri_140,