RetrogeneDB ID: retro_cjac_538

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:69861575..69862208(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000005559
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NOL12
• Ensembl ID: ENSCJAG00000012487
• Aliases: None
• Description: nucleolar protein 12 [Source:HGNC Symbol;Acc:28585]

Sequence

>retro_cjac_538
ATGGGCCGCAACAAGAAGAAGAAGCGAGATAGTGACGAGCGGTGGCCCAGGCTAATTCTCAGCTTCGACGAGGAGAAGAG
GCGGGAGTACCCGACAGGCTTCCACAAGCGGAAGGTCGAGCGGAAGAAGGCGGCCATTGAGGAGATTAAGCAATGGCTGA
AAGAGGAGCAGAGGAGGCTTCAGGAGGAGCGCCACCAGGAATACTTGAAGATGCTGGCAGAGAGAGAAGAGGCACTGGAG
GAGGCCGATGAGCTGGACCGGCTGGTGACAGCAAAGGCGGAGTCGGTGCGGCACGACCACCCCAGCCACACAGTCACCGT
GACCACCATCAGTGACCTGGACCTCTCGGGGACTCAGCTGGTTGGGCTGACCCCACCTGAGGGAGGGGCTGGAGACAGGT
CTGAGAAGGAGGCATCATCCATGGAGAAGCCCACCAAAGCCTTGCCCAGGAAGTCCAGAGACCCCCTGCTCTCTCAGCGG
ATCTCCTCCCTCACAGCAGCACTGCACGCACACAGCCGCAAAAAGGTCAAGAGGAAACATTCCCACAGGGCCCAGGACTC
CAAGAAGCCCCCAGGGGCCTCTCGCACCAGCAGGGCCAAGCGTCGCCGTCTGACAGACAAAGCACAGCACAGC

Alignment

ORF - retro_cjac_538 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 99.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRNKKK-RDGDDRRPRLVLSFDEEKRREYLTGFHKRKVERKKAAIEEIKQRLKEEQRKLREERHQEYLK
          MGRNKKK.RD.D.R.PRL.LSFDEEKRREY.TGFHKRKVERKKAAIEEIKQ.LKEEQR.L.EERHQEYLK
Retrocopy MGRNKKKKRDSDERWPRLILSFDEEKRREYPTGFHKRKVERKKAAIEEIKQWLKEEQRRLQEERHQEYLK

Parental  MLAEREEALEEADELDQLVTAKMESVQYDHPNHTVTVTTISDLDLSGAQLLRVTPPEGGAGDRSEEEASS
          MLAEREEALEEADELD.LVTAK.ESV..DHP.HTVTVTTISDLDLSG.QL...TPPEGGAGDRSE.EASS
Retrocopy MLAEREEALEEADELDRLVTAKAESVRHDHPSHTVTVTTISDLDLSGTQLVGLTPPEGGAGDRSEKEASS

Parental  MEKPTKALPRKSRDPLLSQRISSLTAALHAHSRKKVKRKHPRMAQDSKKPPRAARTSRAQRRRLTGKAQH
          MEKPTKALPRKSRDPLLSQRISSLTAALHAHSRKKVKRKH...AQDSKKPP.A.RTSRA.RRRLT.KAQH
Retrocopy MEKPTKALPRKSRDPLLSQRISSLTAALHAHSRKKVKRKHSHRAQDSKKPPGASRTSRAKRRRLTDKAQH

Parental  S
          S
Retrocopy S

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	4.17 RPM
SRP051959_heart	0.00 RPM	6.89 RPM
SRP051959_kidney	0.00 RPM	5.88 RPM
SRP051959_liver	0.02 RPM	6.71 RPM
SRP051959_lung	0.02 RPM	11.96 RPM
SRP051959_lymph_node	0.05 RPM	16.64 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.31 RPM
SRP051959_spleen	0.00 RPM	10.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_538 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_538 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010139	1 retrocopy	retro_amel_672,
Callithrix jacchus	ENSCJAG00000012487	1 retrocopy	retro_cjac_538 ,
Equus caballus	ENSECAG00000011050	1 retrocopy	retro_ecab_126,
Felis catus	ENSFCAG00000004273	1 retrocopy	retro_fcat_757,
Oryctolagus cuniculus	ENSOCUG00000017013	1 retrocopy	retro_ocun_1698,
Otolemur garnettii	ENSOGAG00000008255	1 retrocopy	retro_ogar_2914,
Pteropus vampyrus	ENSPVAG00000010097	1 retrocopy	retro_pvam_1022,
Tupaia belangeri	ENSTBEG00000009745	1 retrocopy	retro_tbel_3215,
Tursiops truncatus	ENSTTRG00000004799	1 retrocopy	retro_ttru_1165,