RetrogeneDB ID: retro_mmul_904

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:12990711..12991669(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM8A1
• Ensembl ID: ENSMMUG00000001992
• Aliases: None
• Description: protein FAM8A1 [Source:RefSeq peptide;Acc:NP_001245053]

Sequence

>retro_mmul_904
GCCCCTGCAGCAGCCCCCAGGGCCACAACTGCTAACAGGTCAGAGCCACCTGGCAGGCTCAGAAGGAGCCAGGAGGCGAC
CTCTAGCTCCTGTGCGGGGCTGAAGGAGCAGGTGGGGTGTGAAGCATCCAAAGCCATGGTGCTGCAGGAGAGCCAGAGCA
GCTGAGCACCTGTGGGTGCTCCCGGCAAGAGGACGAGTGGCTACAGCAGTCCTGTTGTGGCTACCTCACCTGGCACAGTG
GCCCGGCCACCTTCCCCACCTGCTGCAGCCCCCAAACCCCACAGAGCTTCCCTTCATGTGGCGCTGCTGTCCCCTAGGCC
ATGGTGCCGCCATTCCCGTGGCTGGGCTATTGCAATCCCTTCTACTTCCTGAGCCCTGGGCTGTGGGGCCTGACCCCGGG
GCAGCTGCTGGCATCAGCACCCCTGCTCCAGTCGTGGGCCTGGGACCCCGGGATCCTCAAGTACAGGCATAAGTCTGGGC
CACTCCATTGAGGAAGGTAGGATCTGCAGCCCCTTCATGAAGCCCAAGTGAGACTGGGCAACAGGCAGGCAAAGAATATG
TTATTCCATCATTGGGCCACAGATTTATGGCAAGGATGGTGGATTTCTTTATTCTCTTCTTTGTAAAAGCAACCATTGTC
TTCAGCATTATGCATCACAGTGGGATAAAGGATAGCTCTAAGTTTGCTATGCACCATATAATGGAAGAAATAGATGAAGA
GACATCAATGGAAGACTTTCAGAAAATGATGGTTATGGCTCTTATATACAGATTATTAGTTTGTTTTTATGAGATAATTT
GCATTTGGGGAGCAGGTGGAGCTACCCCAGAGAAGTTCCTCGTGGGGCTTCGAGTTGTGACATGTGATACATTAGTGCTT
ATTGCACTAAGTTGGGTTTTAGTGATTCCTTTCTCAAATGTTAGCATTACAATGTCCACTATACAAGCTTTGATCGAG

Alignment

ORF - retro_mmul_904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.45 %
• Parental protein coverage: 77.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  APGLAAAAAT-DELDSPRELRKRGEAASGSGPGLQEQADCEAPEAAAPRE-RPARLSAREYSRQVHEWLW
          AP..A..A.T......P..LR...EA.S.S..GL.EQ..CEA..A....E..P..LS....SRQ..EWL.
Retrocopy APAAAPRATTANRSEPPGRLRRSQEATSSSCAGLKEQVGCEASKAMVLQE<EPEQLSTCGCSRQEDEWLQ

Parental  QSYCGYLTWHSGLAAFPAYCSPQPSPQSFPSGGAPVPQAAAPPPPQLGYYNPFYFLSPG-AVGPDPRTAA
          QS.CGYLTWHSG.A.FP..CSPQ..PQSFPS.GA.VP.A..PP.P.LGY.NPFYFLSPG.AVGPDP..AA
Retrocopy QSCCGYLTWHSGPATFPTCCSPQ-TPQSFPSCGAAVP*AMVPPFPWLGYCNPFYFLSPG<AVGPDPGAAA

Parental  GISTPAPVAGLGPRAPHVQASVRATPVTRVGSAAPSRSPSETGRQAGREYVIPSLAHRFMAEMVDFFILF
          GISTPAPV.GLGPR.P.VQA.V.ATP...VGSAAPS.SPSETG.QAG.EYVIPSL.HRFMA.MVDFFILF
Retrocopy GISTPAPVVGLGPRDPQVQA*VWATPLRKVGSAAPS*SPSETGQQAGKEYVIPSLGHRFMARMVDFFILF

Parental  FIKATIVLSIMHLSGIKDISKFAMHYIIEEIDEDTSMEDLQKMMVVALIYRLLVCFYEIICIWGAGGATP
          F.KATIV.SIMH.SGIKD.SKFAMH.I.EEIDE.TSMED.QKMMV.ALIYRLLVCFYEIICIWGAGGATP
Retrocopy FVKATIVFSIMHHSGIKDSSKFAMHHIMEEIDEETSMEDFQKMMVMALIYRLLVCFYEIICIWGAGGATP

Parental  GKFLLGLRVVTCDTSVLIAPSRVLVIPSSNVSITTSTIRALIK
          .KFL.GLRVVTCDT.VLIA.S.VLVIP.SNVSIT.STI.ALI.
Retrocopy EKFLVGLRVVTCDTLVLIALSWVLVIPFSNVSITMSTIQALIE

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	13.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.55 RPM
SRP007412_cerebellum	0.00 RPM	11.88 RPM
SRP007412_heart	0.00 RPM	6.18 RPM
SRP007412_kidney	0.00 RPM	8.10 RPM
SRP007412_liver	0.00 RPM	10.69 RPM
SRP007412_testis	0.30 RPM	44.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_904 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_904 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_904 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2166
Pan troglodytes	retro_ptro_1652

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137414	2 retrocopies	retro_hsap_2166, retro_hsap_4922,
Macaca mulatta	ENSMMUG00000001992	1 retrocopy	retro_mmul_904 ,
Monodelphis domestica	ENSMODG00000024641	1 retrocopy	retro_mdom_1866,
Nomascus leucogenys	ENSNLEG00000001130	2 retrocopies	retro_nleu_2828, retro_nleu_460,
Pan troglodytes	ENSPTRG00000017751	2 retrocopies	retro_ptro_1652, retro_ptro_3296,