RetrogeneDB ID: retro_mmul_2043

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:136997548..136998153(+)
• Located in intron of: ENSMMUG00000001726

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS1
• Ensembl ID: ENSMMUG00000003124
• Aliases: None
• Description: None

Sequence

>retro_mmul_2043
ATGGATAGTGTGAATTTTTCCCCTGCCAATTTCTCTAGCACTGGTTCCAGGTATCTGAATGCTTTGGTTGACAGTGTAGT
GGCCCTTGAAACAAAGGATGACTTACCAGCTAGTTTTATCCTTGCAGTGAATGATTTGACCTCTGATCTCTTTCGCACCA
AATCCGAAGGTGAAGAAATCAAGATTGAACTGGAAAAACTTGAAAAAAATCTAACTGCAACTTAATGTTTGAAAAATGTC
TACAAGAGGATCTCAAGAAAGCAGAGTTGCATCTGTCCACAGAAAGGGCCAAAGTTGATACTCGTAGTCAGAACATGAAC
TTTCTAAAAGCAAAGTCAGAGGAATTCAGATTTGGAATCAAGGCTACAGAGGAGCAACTTTCAGCCAGAGGCATGGATGC
TTCTCTGTCTCATCAGTCCTTAGTAGCACTGTCAGAGAAACTGGCCAAATTAAAGCAACAGACTATATCTTTGAAGAAAA
AGTTTGAGTCCTATTTAGACTTAATGCTGAATTCCCCTCTTGCTCAAATGAAAATTGAAGAAGCAAAGCAAGAATTAGAC
AGCAATGAAGCTGAACTTACAAGGAGAGTAGACATGATGGAACTG

Alignment

ORF - retro_mmul_2043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MESVNFSPANLSSTGSRYLNALVDSSVALETKDTSLASFIPAVNDLTSNLFRTKSKSEEIKIELEKLEKN
          M.SVNFSPAN.SSTGSRYLNALVDS.VALETKD...ASFI.AVNDLTS.LFRTKS..EEIKIELEKLEKN
Retrocopy MDSVNFSPANFSSTGSRYLNALVDSVVALETKDDLPASFILAVNDLTSDLFRTKSEGEEIKIELEKLEKN

Parental  LTAT-LVLEKCLQEDVKKAELHQSIERAKVDNRRQNMDFLKAKSEEFRFGIKAAEEQLSARGMDASLSHQ
          LTAT.L..EKCLQED.KKAELH.S.ERAKVD.R.QNM.FLKAKSEEFRFGIKA.EEQLSARGMDASLSHQ
Retrocopy LTAT<LMFEKCLQEDLKKAELHLSTERAKVDTRSQNMNFLKAKSEEFRFGIKATEEQLSARGMDASLSHQ

Parental  SLVALSEKLARLKQQTIPLKKKLESYLDLMPNPSLARVKIEEAKRELDSIEAELTRRVDMMEL
          SLVALSEKLA.LKQQTI.LKKK.ESYLDLM.N..LA..KIEEAK.ELDS.EAELTRRVDMMEL
Retrocopy SLVALSEKLAKLKQQTISLKKKFESYLDLMLNSPLAQMKIEEAKQELDSNEAELTRRVDMMEL

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
SRP007412_brain	0.00 RPM	4.15 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.46 RPM
SRP007412_cerebellum	0.00 RPM	8.46 RPM
SRP007412_heart	0.00 RPM	2.89 RPM
SRP007412_kidney	0.00 RPM	3.64 RPM
SRP007412_liver	0.00 RPM	1.19 RPM
SRP007412_testis	0.00 RPM	4.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2043 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2043 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3247
Pan troglodytes	retro_ptro_2195
Gorilla gorilla	retro_ggor_2210
Pongo abelii	retro_pabe_2693

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001139	3 retrocopies	retro_chof_237, retro_chof_2496, retro_chof_255,
Homo sapiens	ENSG00000152240	3 retrocopies	retro_hsap_3247, retro_hsap_4075, retro_hsap_4655,
Gorilla gorilla	ENSGGOG00000010098	2 retrocopies	retro_ggor_2210, retro_ggor_2888,
Loxodonta africana	ENSLAFG00000010897	1 retrocopy	retro_lafr_1063,
Macaca mulatta	ENSMMUG00000003124	2 retrocopies	retro_mmul_2043 , retro_mmul_2476,
Monodelphis domestica	ENSMODG00000003208	1 retrocopy	retro_mdom_743,
Nomascus leucogenys	ENSNLEG00000011216	3 retrocopies	retro_nleu_1091, retro_nleu_1698, retro_nleu_2043,
Pongo abelii	ENSPPYG00000009131	3 retrocopies	retro_pabe_2693, retro_pabe_3344, retro_pabe_3615,
Pan troglodytes	ENSPTRG00000009992	3 retrocopies	retro_ptro_2195, retro_ptro_2762, retro_ptro_3092,
Tupaia belangeri	ENSTBEG00000010911	4 retrocopies	retro_tbel_1209, retro_tbel_1348, retro_tbel_3868, retro_tbel_4672,