RetrogeneDB ID: retro_mmul_1342

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:5942879..5944416(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFWD2
• Ensembl ID: ENSMMUG00000002072
• Aliases: None
• Description: E3 ubiquitin-protein ligase RFWD2 [Source:RefSeq peptide;Acc:NP_001253194]

Sequence

>retro_mmul_1342
AGCCACCACGCCAGGTCAGACTCCACTGGGACGAGCCCCTGCTCCTCATGCTCTTTGGTGACTTTTGCCTCCTTGTCCTT
ATCATCTTCCCCATTGCCACCACTATGGCAGCTTTGGCTGCTGTCCAGCGGGGTGGCCCAGGCCACCAGCTTGGATAGCC
CTGGGGCCCAGTGTGGCCGTGTTGGTGGTGCCCACTGTGTCAGGCAGTGGCAGGGTGGTATCCATAGTCCTGTCCCAGCT
CAGCTGCGTGTCCAGGCCCAGTGCTGGTATAGGAGGCAGCAGCTGTAGACTAGGCAGCAGCAGGAAGCAACCTCTGCTTG
CCCCTCCCCTCTGTATCAGGCTCATCCACTCATATAAGGACAACAGCAATGATTTCATATGCCCCATCTGCTTTGATATG
ATTGAAGAGGCATACATGACAAAATGTGGCCACAGCTTTTGCTGTAAGTATATTCATCAGAGTTTGGAGGACAATAATAG
ATGTAGCAAGTGTGACTATGTTGTGGACTATACTAACCATCTGTTTCCTAATTTGTTGGTGAACGAGCTCATTCTCAAAC
AGAGCAAAGATCTAAGGAAAAGAGGTTCAAACTGGACCACTCAGTGAGTAGCACCTATGGCCACAGATGGTGAATATCTC
AAGATTTGTTGGGAACTGACCAAGATAACCTTGATTTGGCCAATATCAACCTCATGTTGGAGCTACTAGTGCAGAAGAAG
AAACAACTGGAAGCAGAATCACATACAGCCCAACTACAGAATCTTATACAATTCCTCAAGATTGCAAGAAGAAATAGGAG
AGAACAACTGGGACAGTTGCAGAAGGAGCTACATGTTCTGGAAGAGGATATTAAAAGAGTGGAAGAAATGAGTGGCTTAT
ACTCTCCTGTCAGTGAGAATAGCACAGAGCCTCAACTTGAAGCTCCTCCTGCGTCACACAGTAGCGTTATGGATTCCACA
GGATATAGCCAACATCCAGGTTTCAGTGGCAGTTCTTAGACAAAGAAACAGCCTTGACATAACAGCACATTAGCGTCAAA
ATGAAAATGGCCCACTGCTCATTTTGAAGACCTGGAGCAGTGTTACTTTTCTACAAGGATGTCTCACGTCTCAGATGATA
GTCGAACTGCCAGCCAATTGGATGAATTTCAGAAATGCTTGTCCAAGGTTACTCAGTATAAATTGGTACAAACTTTAACC
ACATTATCATGCCCTAGTGATCTCTATAATGATTCCAGGATAGTCTCTGGTATTGAATTTGACCAGGATTGTGACTATTT
TGCAATTCCTGAGGTTACAATGAAGATTAAAGTCTATGAATATGGCACTGCATCCAGGATGCAGTGGATATTCATTACCG
TGTGAATGAAATGACCTCAATTCCAAAATCAGCTGTATCAGTTGGAGTAGTTACCATAAGAATCTGTTAGCTAGCAGTGA
TTATGAAGGCATTGTTATCCTATGGGATGGATTCACAGGATAGAGGTCAAAGGTCTAACAGGAGCATGAGAAGAGGTGTG
GAAGTGTTTAATTTGAT

Alignment

ORF - retro_mmul_1342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.05 %
• Parental protein coverage: 71.0 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPPSVAASAAALVSGGAAQPAGSGGLG-GPVRP-VLVA
          S..A.S.S.GTSP.SS..S.VT.A..SLS.S.S.P........L.S.G.AQ.......G.GPV.P.VLV.
Retrocopy SHHARSDSTGTSPCSSC-SLVTFA--SLSLSSS-PLPPLWQLWLLSSGVAQATSLDSPG<GPVWP<VLVV

Parental  PAVSGSGGGAVSTGLSRHSCVARPSAGVGGSSSSLGSGSRKRPLLAP-LCNGLINSYEDKSNDFVCPICF
          P.VSGSG...VS..LS..SCV.RPSAG.GGSS..LGS.SRK.PLLAP.LC..LI.SY.D.SNDF.CPICF
Retrocopy PTVSGSGR-VVSIVLSQLSCVSRPSAGIGGSSCRLGS-SRKQPLLAPPLCIRLIHSYKDNSNDFICPICF

Parental  DMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNIDHLYPNFLVNELILKQ-KQRFEEKRFKLDH
          DMIEEAYMTKCGHSFC.K.IHQSLEDNNRC.KC.YVVD...HL.PN.LVNELILKQ..QR..EKRFKLDH
Retrocopy DMIEEAYMTKCGHSFCCKYIHQSLEDNNRCSKCDYVVDYTNHLFPNLLVNELILKQ<EQRSKEKRFKLDH

Parental  SVSSTNGHRWQIFQDLLGTDQDNLDLANVNLMLELLVQKKKQLEAESHAAQLQILMEFLKVARRNKREQL
          SVSST.GHRW.I.QDLLGTDQDNLDLAN.NLMLELLVQKKKQLEAESH.AQLQ.L..FLK.ARRN.REQL
Retrocopy SVSSTYGHRW*ISQDLLGTDQDNLDLANINLMLELLVQKKKQLEAESHTAQLQNLIQFLKIARRNRREQL

Parental  EQIQKELSVLEEDIKRVEEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPWY
          .Q.QKEL.VLEEDIKRVEEMSGLYSPVSE.ST.PQ.EAP..SHSS..DST.YSQ.PGFSGSS.TKKQP..
Retrocopy GQLQKELHVLEEDIKRVEEMSGLYSPVSENSTEPQLEAPPASHSSVMDSTGYSQHPGFSGSS*TKKQP*H

Parental  NSTLASRRKRLTAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYN
          NSTLAS..K..TAHFEDLEQCYFSTRMS..SDDSRTASQLDEFQ.CLSK.T.Y..V..L.TLS..SDLYN
Retrocopy NSTLASK*KWPTAHFEDLEQCYFSTRMSHVSDDSRTASQLDEFQKCLSKVTQYKLVQTLTTLSCPSDLYN

Parental  GSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYGTV-IQDAVDIHYPENEMT-CNSKISCISWSSYHKNLLA
          .S.IVS.IEFD.DCDYFAI..VT.KIKVYEYGT..IQDAVDIHY..NEMT..NSKISCISWSSYHKNLLA
Retrocopy DSRIVSGIEFDQDCDYFAIPEVTMKIKVYEYGTA<IQDAVDIHYRVNEMT<LNSKISCISWSSYHKNLLA

Parental  SSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFN
          SSDYEG.VILWDGFTG.RSKV.QEHEKRC.SV.F.
Retrocopy SSDYEGIVILWDGFTG*RSKV*QEHEKRCGSV*FD

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	22.30 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	17.14 RPM
SRP007412_cerebellum	0.00 RPM	16.98 RPM
SRP007412_heart	0.06 RPM	10.54 RPM
SRP007412_kidney	0.00 RPM	15.14 RPM
SRP007412_liver	0.00 RPM	10.33 RPM
SRP007412_testis	0.00 RPM	20.24 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1342 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1342 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1281
Gorilla gorilla	retro_ggor_1366

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000013437	1 retrocopy	retro_ggor_1366,
Macaca mulatta	ENSMMUG00000002072	1 retrocopy	retro_mmul_1342 ,
Macaca mulatta	ENSMMUG00000009940	1 retrocopy	retro_mmul_75,
Mus musculus	ENSMUSG00000040782	1 retrocopy	retro_mmus_3678,
Nomascus leucogenys	ENSNLEG00000015420	1 retrocopy	retro_nleu_1225,
Pan troglodytes	ENSPTRG00000001711	1 retrocopy	retro_ptro_1281,