RetrogeneDB ID: retro_mmul_1177

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:33693888..33694823(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18535
• Ensembl ID: ENSMMUG00000019720
• Aliases: None
• Description: protein FAM190B [Source:RefSeq peptide;Acc:NP_001180691]

Sequence

>retro_mmul_1177
GAGAAAATAAACACAAAAGATGAAAAGATCCAACAAATAGAACTTCAGCTTGCAATTTACTATAACCACCACCAAAAATT
AAGGAGGAAAAATGCACACATACTGATAAATATACCAAAACACCCTGGAAACAAATTCCTCCTCAAGTGCTACAACCTTC
CAGCAGCCTTCCCAGACCAACAGACCATGCCAGGAGAGAATGAATATAGCCACAACATAGGGAGATCCCCAGCGAAGGTG
CAATCCAAGACATGTGTCAGGGCTTCGCATATCTGGATGAAGGTTTTACATATGACTTGCAATAAGAAAGCAACTATGGT
TTGGAAAACCAGCCTTTTTCATCAGGCCCACATTAACAATGGATGTGGCTAAGAGTACATTTTCTGAAACAAACTTCAAC
ATGACTGTAAATGCTTAAGAGCCTTATCATTTGCCAAGTGATAAAATTAGTGACATGCAGTTTATACCCACTTTTCTTCA
GACACCTCTCCAGTCTAGTACAGTAGACCAGGCTAAGAGAGTTAGAAGCTGTACATTTCATCTCATGTCCTTGCAGCTTT
TAAAGCCATCCATCTTGATTCTGTGATACCTCCTCCAGTTTCTGAATCATCTCCAAGCAGGACTCCCACTTGGAAGAAGT
CTTTGATAATCACAGCATGTAACTCAGCAAAACTTCAGTCAACATCAAATAAGAAAAATAATCGTACAACTAATCGGAAT
CTGAGAGTGCCTAAGCTCTGCCACCCTTCAGGTTCTTTCAAACAAAAACAAATAAACAACCTCCAACAAGAGCCTCAAAG
CTTCTAAGCCAAACAAGCATCTCAAACACACTAAGACAAAGAAAATAAATCATGTAGAACCCAAATGGCAATTTACATTT
TGGGGATTCTTTGGCCTCTAATCATTATTCCAGTCTTCTTAAACCAAAGATATAT

Alignment

ORF - retro_mmul_1177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EEIKKKDEKIQLLELQLATQHICHQKC-KEEKCTYADKYTQTPWRRIPPQVLQPSSSLPRPTDHTQGKLI
          E.I..KDEKIQ..ELQLA.....HQK..KEEKCT..DKYT.TPW..IPPQVLQPSSSLPRPTDH.....I
Retrocopy EKINTKDEKIQQIELQLAIYYNHHQKL<KEEKCTHTDKYTKTPWKQIPPQVLQPSSSLPRPTDHARRE*I

Parental  KPQHIEAHSECAIQDMHQGVAHLEESFTQVLQQESNYGLEEQPFSSGPQ-LTMDVAKSTPSEAN-NITVN
          .PQH.E..SE.AIQDM.QG.A.L.E.FT..LQ.ESNYGLE.QPFSSGP..LTMDVAKST.SE.N.N.TVN
Retrocopy *PQHREIPSEGAIQDMCQGFAYLDEGFTYDLQ*ESNYGLENQPFSSGPH<LTMDVAKSTFSETNFNMTVN

Parental  A-QSYH-GNNQISDMQ-LYPLLQTLPSSTVDAKRVENQSRQWYVSQPSL-QLKPSIL-SSLVPPPVSESS
          A...YH.....ISDMQ.LYPL.....SS.V...R..........S.P....LKPSIL..S..PPPVSESS
Retrocopy A*EPYHLPSDKISDMQ>LYPLFFRHLSSLVQ*TRLRELEAVHFISCPCS<LLKPSIL<DSVIPPPVSESS

Parental  PSRTSTCKKSPIVATCNSAKLQPTSSQ-TNLANNQNLKASKLRPPSGSFKQKQTNSPQLEPQSFQAK-TS
          PSRT.T.KKS.I...CNSAKLQ.TS....N...N.NL...KL..PSGSFKQKQ.N..Q.EPQSF.AK.TS
Retrocopy PSRTPTWKKSLIITACNSAKLQSTSNKKNNRTTNRNLRVPKLCHPSGSFKQKQINNLQQEPQSF*AK<TS

Parental  IPRPLTQRKEIMQNPNGNLHSGDCLASNRYSRLPKPKIH
          I...L.QRK.IM.NPNGNLH.GD.LASN.YS.L.KPKI.
Retrocopy ISNTLRQRK*IM*NPNGNLHFGDSLASNHYSSLLKPKIY

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	0.34 RPM	53.90 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	38.55 RPM
SRP007412_cerebellum	0.19 RPM	42.68 RPM
SRP007412_heart	0.06 RPM	21.67 RPM
SRP007412_kidney	0.00 RPM	16.55 RPM
SRP007412_liver	0.00 RPM	5.15 RPM
SRP007412_testis	1.17 RPM	213.57 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1177 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000019720	1 retrocopy	retro_mmul_1177 ,