RetrogeneDB ID: retro_mmul_2432

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:11015421..11015773(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12783
• Ensembl ID: ENSMMUG00000014316
• Aliases: None
• Description: ORM1-like protein 1 [Source:RefSeq peptide;Acc:NP_001253278]

Sequence

>retro_mmul_2432
ATTGTCTTACTCAGCATTCCTTCTTCTGTGTTCTCATTGCTTAGACCTTAACAAATATTATACGTAATCTGGGGATGAAT
GGATGTTTCCATGCTTGAAAGGAATGCCTTTGGAAACCCCTGACCAGGGTAAAGCAAGGCTCCTAACGCACTGAGAACAA
CTGGGTGAGGGAGTACCATTTACATCTTCACGGAAGTTTTTCACCATTTCTCCAATCATTCTGCATTTTCCAGCAAGTTT
CTATAGAAGTATGCTCCAACTCACTCCATTGTAAGCACAGCTTCTCTCCTGAGTACGCTAAACTCCCCAAATGCCACAAC
GACACGGTGCTCCGATCTTTGGAATTAATAAG

Alignment

ORF - retro_mmul_2432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.95 %
• Parental protein coverage: 77.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IVLLSIP-FFSVPVAWTLTNIIHNLGMYVFLHA-VKGTPFETPDQGKARLLTHWEQLDYGVQFTSSRKFF
          IVLLSIP.FF.V..A.TLTNII.NLGM....HA..KG.P.ETPDQGKARLLTH.EQL..GV.FTSSRKFF
Retrocopy IVLLSIP<FFCVLIA*TLTNIIRNLGMNGCFHA<LKGMPLETPDQGKARLLTH*EQLGEGVPFTSSRKFF

Parental  TISPIILYFLASFYT-KYDPTHFILNTASLLSVL-IPKMPQLHGVRIFGINK
          TISPIIL.F.ASFY..KY.PTH.I..TASLLS.L..P.MPQ.HG..IFGINK
Retrocopy TISPIILHFPASFYR<KYAPTHSIVSTASLLSTL>TPQMPQRHGAPIFGINK

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	0.22 RPM	21.40 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	16.58 RPM
SRP007412_cerebellum	0.00 RPM	27.38 RPM
SRP007412_heart	0.00 RPM	11.54 RPM
SRP007412_kidney	0.00 RPM	15.96 RPM
SRP007412_liver	0.00 RPM	9.26 RPM
SRP007412_testis	0.00 RPM	18.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2432 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2432 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_645
Pan troglodytes	retro_ptro_469
Gorilla gorilla	retro_ggor_565

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005579	1 retrocopy	retro_cjac_2962,
Homo sapiens	ENSG00000128699	1 retrocopy	retro_hsap_645,
Gorilla gorilla	ENSGGOG00000015259	1 retrocopy	retro_ggor_565,
Loxodonta africana	ENSLAFG00000007769	1 retrocopy	retro_lafr_411,
Myotis lucifugus	ENSMLUG00000014339	1 retrocopy	retro_mluc_2318,
Macaca mulatta	ENSMMUG00000006292	1 retrocopy	retro_mmul_2358,
Macaca mulatta	ENSMMUG00000014316	1 retrocopy	retro_mmul_2432 ,
Nomascus leucogenys	ENSNLEG00000006625	1 retrocopy	retro_nleu_730,
Pongo abelii	ENSPPYG00000013017	2 retrocopies	retro_pabe_570, retro_pabe_571,
Pan troglodytes	ENSPTRG00000012736	1 retrocopy	retro_ptro_469,
Sus scrofa	ENSSSCG00000016044	1 retrocopy	retro_sscr_247,
Tupaia belangeri	ENSTBEG00000012942	1 retrocopy	retro_tbel_10,
Tursiops truncatus	ENSTTRG00000005240	2 retrocopies	retro_ttru_1846, retro_ttru_770,