RetrogeneDB ID: retro_mmul_1499

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:21091774..21092390(-)
• Located in intron of: ENSMMUG00000002865

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM175A
• Ensembl ID: ENSMMUG00000015357
• Aliases: None
• Description: family with sequence similarity 175, member A [Source:HGNC Symbol;Acc:25829]

Sequence

>retro_mmul_1499
CACAGCTCTACATTTTTTGAAGAAGATGGATCTTTAAAGGAGGTACATAAGATAAAGGAAATGTATGCTTCATTACAAGA
GGAATTAAGAGTATATGCAAAAAAGTGGAAGACAGTGAACAAGCAATAAATAAACTAGTAAAGGATGTAAACAGATTAAA
ACAAGAAACTGAGAAAAGGAGATGAGCATAGATTCAGGCAGCAGGAGAGAAGAACATCTAAAAAGACCCTCAGGGGAACA
TTTTTCCTGGTCAAGCATTGCGGACCTTTTATCCAGATTCTGAATTTCTTCAATCATGTGTTATGTCTTTAAAAACCAGA
CATGTTTCTAAAAGTAGCTGTAACTACTACCTCCACCTCGATGTAGTAGCCAAAATGACCTTAATGGTAGAACACACTGA
CATTCCTGAAGCTAGTCCAGCTAGCAGACCACAAATGATTAAGCATAAAGCTTTAGGCTTAGATGACAGATGAAATTCAA
GAGATCATGGCAGTTAGAGATACAAGACAAACCATCTAAAACAGATACTGATAGTAGTTACCAAGAAAAAGCATCCACAA
TGGACAGCCCAGAAATAGATGAAGAGATTGAGAAAATGAAGGGATCTAGTGAATAT

Alignment

ORF - retro_mmul_1499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 97.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YSSKFFEEDGSLKEVHKINEMYASLQEEL-KSICKKVEDSEQAVDKLVKDVNRLKREIEKRKRAQIQAAR
          .SS.FFEEDGSLKEVHKI.EMYASLQEEL.KSICKKVEDSEQA..KLVKDVNRLK.E.EKR..A.IQAA.
Retrocopy HSSTFFEEDGSLKEVHKIKEMYASLQEEL<KSICKKVEDSEQAINKLVKDVNRLKQETEKRR*A*IQAAG

Parental  EKNIQKDPQENIFLCQALRTFFPNSEFLHSCVMSLKSRHVSKSSCNINHHLDVVDNLTLMVEHTGIPEAS
          EKNI.KDPQ.NIF..QALRTF.P.SEFL.SCVMSLK.RHVSKSSCN...HLDVV...TLMVEHT.IPEAS
Retrocopy EKNI*KDPQGNIFPGQALRTFYPDSEFLQSCVMSLKTRHVSKSSCNYYLHLDVVAKMTLMVEHTDIPEAS

Parental  SASTPQIIKHKALDLDDR-WQFKRSRLLDTQDERSKADTDSSNQDKASKMSSPETDEEIEKMKGFGEY
          .AS.PQ.IKHKAL.LDDR...FKRS..L..QD..SK.DTDSS.Q.KAS.M.SPE.DEEIEKMKG..EY
Retrocopy PASRPQMIKHKALGLDDR<MKFKRSWQLEIQDKPSKTDTDSSYQEKASTMDSPEIDEEIEKMKGSSEY

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	0.90 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.63 RPM
SRP007412_cerebellum	0.00 RPM	1.87 RPM
SRP007412_heart	0.06 RPM	0.82 RPM
SRP007412_kidney	0.00 RPM	2.46 RPM
SRP007412_liver	0.00 RPM	0.67 RPM
SRP007412_testis	0.00 RPM	3.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1499 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1499 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1911
Pongo abelii	retro_pabe_2208

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013241	1 retrocopy	retro_chof_2580,
Homo sapiens	ENSG00000163322	1 retrocopy	retro_hsap_4024,
Gorilla gorilla	ENSGGOG00000005818	1 retrocopy	retro_ggor_2701,
Macaca mulatta	ENSMMUG00000015357	2 retrocopies	retro_mmul_1499 , retro_mmul_2320,
Nomascus leucogenys	ENSNLEG00000009133	2 retrocopies	retro_nleu_1198, retro_nleu_661,
Pongo abelii	ENSPPYG00000014898	2 retrocopies	retro_pabe_2208, retro_pabe_3301,
Pan troglodytes	ENSPTRG00000023645	2 retrocopies	retro_ptro_1911, retro_ptro_2728,