RetrogeneDB ID: retro_mmul_2158

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:76672846..76674162(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM149B1
• Ensembl ID: ENSMMUG00000011281
• Aliases: None
• Description: protein FAM149B1 [Source:RefSeq peptide;Acc:NP_001248682]

Sequence

>retro_mmul_2158
GGAATAACAAAACATGCTCTTAACCATCATCCCTCTCCCAAGAAGCTAGAGGAAATTTCCCTGCCAGTGACAGTCATGAG
AAAGACACAAGTTCCCAAAGCGAGTCTGACATCACAAGAGAATCACCTTTTACATCAGCCGACGCTGGGAATTCACTCTC
TGCTTTTCCAAGTTATACAGGCGCAGGGATATCTACTGAAGGCAGCTCGGACTTCTCCTGGGGATATGGTGAACTCGATC
AAAATGCCACTGAAAAAGCCTAGGCAATGTTCACAGCCGTCGATGAACTCTTGTATGAGCAGAAGTTGAGTGTGCATAAC
AAGAGTCTACAAGAAGAGTGCCAACAGTGAATAGCTAGCTTTCCTCACCTCAGGATTCTAGGTAGGCAGACAATCACTCC
AAGTGAAGGTTATAGATTGTATCCTAGATCCCCTTCTGCTGTTTCAGCTTCATATGAAACAACCTTGTCTCAAGAAAGAG
ATTCTACTATATTTGGTATAAGGGGAAAGAAGTTACGTTTTTCATCTTCGTATGCTCATAAAGCATCTTCTATTGCCAAA
TCCTCCAGCTTTTGTTCTATGGAAAGAGACGAGGAAGACTCTATAATCATCTCGGAAGGAGTAATTGAGGAATACCTAGC
ATTTGATCACACAGATATGTAAGAGGGATTTCATGGGAAGAAATCAGGAGCAGCTACAGAGAAACAGAAATGAGGGTATC
CTCCCATTGCTCCATTTTACTGTGTGAAAGAAGATGTCCTTGTTTATGTGTTTGACAATGTATGGAGCAAGGTTGTGAGC
TGTATGGAACAGTTGACACGTAGTCACTGGGAAGGATTTGCCTCTGATGATGAGAGTAATGTTGCAGTTCCCAGACCCGA
TTCAAAAAGTTCTTGTGTGCTGAGTGAACCACATCCTTTGGTGTTACCGTGAGTGCCACAGTCTAAGGTACTGTCCGTTA
CTTCAAATCCAATGAGTCTCTGTGAAGCAAGCAGTCATCAGCCAAATGTGAATGGTCTCTTGGTTCATGGGATGCCTCTA
CAGGCAAGAAATAGCTCCCTAATGGACAAGCTCCTAGATCTTGATGACAAGCTACTTCTGAGGCCAGGTTCCAGTACCAT
CCTTTCAATTCGAAGTTGGCCAAATCGAGCTGTGGAGTTTAGTACATCATCTCTGTCATACACAGTGCAGTCCACTAAGA
GAGGCAATCCATCGCCACGAACCTTTCATCCGATCAGCACAAGGCATTCACAGGCTGGAATACCAAGACGTGTGGAAGAA
ATCCTTAGAGGAGCCCCAGTCCCAGCGGCAGCGGAA

Alignment

ORF - retro_mmul_2158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.95 %
• Parental protein coverage: 77.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GITKHALNHRPPPEKLEDVS-PTSDSHEKDTSSQSKSDITRESSFTSADTGNSLSAFPSYSGAGISTEGS
          GITKHALNH.P.P.KLE..S.P.SDSHEKDTSSQS.SDITRES.FTSAD.GNSLSAFPSY.GAGISTEGS
Retrocopy GITKHALNHHPSPKKLEEIS<PASDSHEKDTSSQSESDITRESPFTSADAGNSLSAFPSYTGAGISTEGS

Parental  SDFSWGYGELDQNATEKVQAMFTAIDELLYEQKLSVHTKSLQEECQQWTASFPHLRILGRQIITPSEGYR
          SDFSWGYGELDQNATEK..AMFTA.DELLYEQKLSVH.KSLQEECQQ..ASFPHLRILGRQ.ITPSEGYR
Retrocopy SDFSWGYGELDQNATEKA*AMFTAVDELLYEQKLSVHNKSLQEECQQ*IASFPHLRILGRQTITPSEGYR

Parental  LYPRSPSAVSASYETTLSQERDSTIFGIRGKKLHFSSSYAHKASSIAKSSSFCSMERDEEDSIIFSEGII
          LYPRSPSAVSASYETTLSQERDSTIFGIRGKKL.FSSSYAHKASSIAKSSSFCSMERDEEDSII.SEG.I
Retrocopy LYPRSPSAVSASYETTLSQERDSTIFGIRGKKLRFSSSYAHKASSIAKSSSFCSMERDEEDSIIISEGVI

Parental  EEYLAFDHTDMKEGFHGKKSEAATEKPKLGYPPIAPFYCIKEDVLAYVFDNVWSKVVSCMEELTRSHWEG
          EEYLAFDHTDM.EGFHGKKS.AATEK.K.GYPPIAPFYC.KEDVL.YVFDNVWSKVVSCME.LTRSHWEG
Retrocopy EEYLAFDHTDM*EGFHGKKSGAATEKQK*GYPPIAPFYCVKEDVLVYVFDNVWSKVVSCMEQLTRSHWEG

Parental  FASDDESDVAITRPDSESSCVLSEPHPLVLPRVPQSKVLSITSNPMSLCQASSHQPNVNGLLVHGMPLQP
          FASDDES.VA..RPDS.SSCVLSEPHPLVLP.VPQSKVLS.TSNPMSLC.ASSHQPNVNGLLVHGMPLQ.
Retrocopy FASDDESNVAVPRPDSKSSCVLSEPHPLVLP*VPQSKVLSVTSNPMSLCEASSHQPNVNGLLVHGMPLQA

Parental  RNLSLMDKLLDLDDKLLMRPGSSTILSTRNWPNRAVEFSTSSLSYTAQSTRRRNPPPRTLHPISTSHSRA
          RN.SLMDKLLDLDDKLL.RPGSSTILS.R.WPNRAVEFSTSSLSYT.QST.R.NP.PRT.HPIST.HS.A
Retrocopy RNSSLMDKLLDLDDKLLLRPGSSTILSIRSWPNRAVEFSTSSLSYTVQSTKRGNPSPRTFHPISTRHSQA

Parental  GTPRPMEEILRGARVPVAAD
          G.PR..EEILRGA.VP.AA.
Retrocopy GIPRRVEEILRGAPVPAAAE

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	0.11 RPM	15.13 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	12.38 RPM
SRP007412_cerebellum	0.00 RPM	13.50 RPM
SRP007412_heart	0.06 RPM	8.19 RPM
SRP007412_kidney	0.12 RPM	19.01 RPM
SRP007412_liver	0.00 RPM	8.23 RPM
SRP007412_testis	5.73 RPM	34.00 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2158 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2158 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138286	1 retrocopy	retro_hsap_1529,
Macaca mulatta	ENSMMUG00000011281	1 retrocopy	retro_mmul_2158 ,
Nomascus leucogenys	ENSNLEG00000016575	1 retrocopy	retro_nleu_1938,
Pan troglodytes	ENSPTRG00000002623	2 retrocopies	retro_ptro_1036, retro_ptro_2950,
Rattus norvegicus	ENSRNOG00000006554	1 retrocopy	retro_rnor_2124,
Ictidomys tridecemlineatus	ENSSTOG00000002142	1 retrocopy	retro_itri_429,