RetrogeneDB ID: retro_mmul_1741

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:187442506..187443761(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4771
• Ensembl ID: ENSMMUG00000018141
• Aliases: STRADB, ALS2CR2
• Description: STE20-related kinase adapter protein beta [Source:RefSeq peptide;Acc:NP_001252850]

Sequence

>retro_mmul_1741
GTGTCTCCTTTGGATTGTTTCTGCACTTCAAGAACACAGGTTGGATCACTCAAACCCAAAACACAAACCTGAAACCAGCA
TCCATCAATACTTGGTCGATGAGCCAACCCTTTCCTGGTCGGGTCCATCCACTAGAGCCAGTGAAGTAGTATGTTCCATC
AACATTTCTCACTATGAGCTCCAAGTAGAAATAGGAAGAGGATTTGACAACTTGACTTCTGTCCATCTTGCACGGCATAC
TCCTACAGGAACACTGGTAACTATAAAAGTTACAAATCTGGAAAACTGCAATGAAGAATGTCTGAAAGTTTTACAGAAAG
CCATGATTCTATCCCACTTTTTCTGGCATCCCAATATTACAACTTATTGGACAGTTTTCAGTGTTGACAGCTGGCTTTGA
GTTATTTCTCCATTTATGGCCTATGGTTCAGCAAGTCAACTCTTGAGGGCCTATTTTCCTGAAGGAATGGGTAAAACTTT
AATAAGAAACATTCTCTTTGGAGCAGTGAGAGGACTGAACTATCTGCACCAATATGGCTGTATTCATAGGAGTAGTAAAG
CCAGCCATATCCTCATTTCTGATGATGGCCTAGTGACCCTCTCTGGCCTGTCTCATCTGCATAGTTTGGTTAAGCATGGA
CAGAGCCATAGGGCTGTGTATGATTTCCCACAGTTCAGCACATCAGTGCAACCATGGCTGAGTCCAGAACTACTGAGACA
GGATTTACATGGGTATAATGTGAAGTCAGATATTTACAGTGTTGGGATTACAACATGTGAATTAGCCAGTACGCAGGTGC
CTTTCCAGGATATGAAGAGAACTCAGATGCTGTTACAGAAACTGAAAGTTCCCCCTTATAGCCCATTGGATATCAGTATT
TTCCCACAATCAGAATCCAAAATGAAAGATTCCCGGTCAGGTGTAGACTCTGGGATTGGAGCAAGGGTGCTTATCTCCAG
TGGAACTCACACAGTAAATAGTGACCGATTACGCACACCATCCTCAAAAACCGTCTCTCCTGCCTTATTTAGCTTTTTGC
CACTGTGTTTGCAACAAGATCTGGAGAAAAGGCCATCAGCAAGCAGTTTATAGTCCCATGTTTTCTTCAAACAGATGAAA
GAAGATAGCCAGGATTCAATACTTTCACTGTTGCCTCCTGCTTATAACAAGCCATCAGTGTCATTGCCTCCAGTGTTACC
CTGGACTGAGCCAGATTGTGATTTTCCTGATGAAAAAGACTCATATTGGGAATTC

Alignment

ORF - retro_mmul_1741 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLLDCFCTSRTQVESLRPEKQS-ETSIHQYLVDEPTLSWSPPSTRASEVVCSTNVSHYELQVEIGRGFD
          .S.LDCFCTSRTQV.SL.P..Q..ETSIHQYLVDEPTLSWS.PSTRASEVVCS.N.SHYELQVEIGRGFD
Retrocopy VSPLDCFCTSRTQVGSLKPKTQT>ETSIHQYLVDEPTLSWSGPSTRASEVVCSINISHYELQVEIGRGFD

Parental  NLTSVHLARHTPTGTLVTIKITNLENCNEERLKALQKAVILSHFFRHPNITTYWTVFTVGSWLWVISPFM
          NLTSVHLARHTPTGTLVTIK.TNLENCNEE.LK.LQKA.ILSHFF.HPNITTYWTVF.V.SWL.VISPFM
Retrocopy NLTSVHLARHTPTGTLVTIKVTNLENCNEECLKVLQKAMILSHFFWHPNITTYWTVFSVDSWL*VISPFM

Parental  AYGSASQLLRTYFPEGMSETLIRNILFGAVRGLNYLHQNGYIHRSIKASHILISGDGLVTLSGLSHLHSL
          AYGSASQLLR.YFPEGM..TLIRNILFGAVRGLNYLHQ.G.IHRS.KASHILIS.DGLVTLSGLSHLHSL
Retrocopy AYGSASQLLRAYFPEGMGKTLIRNILFGAVRGLNYLHQYGCIHRSSKASHILISDDGLVTLSGLSHLHSL

Parental  VKHGQRHTAVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGITACELASGQVPFQDMHRTQMLLQ
          VKHGQ.H.AVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGIT.CELAS.QVPFQDM.RTQMLLQ
Retrocopy VKHGQSHRAVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGITTCELASTQVPFQDMKRTQMLLQ

Parental  KLKGPPYSPLDISIFPQSESRMKNSRSGVDSGIGESVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLVQLC
          KLK.PPYSPLDISIFPQSES.MK.SRSGVDSGIG..VL.SSGTHTVNSDRL.TPSSKT.SPA.FS...LC
Retrocopy KLKVPPYSPLDISIFPQSESKMKDSRSGVDSGIGARVLISSGTHTVNSDRLRTPSSKTVSPALFSFLPLC

Parental  LQQDPEKRPSASSLLSHVFFKQMKEESHDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDEKDSYWEF
          LQQD.EKRPSASSL.SHVFFKQMKE.S.DSILSLLPPAYNKPS.SLPPVLPWTEP.CDFPDEKDSYWEF
Retrocopy LQQDLEKRPSASSL*SHVFFKQMKEDSQDSILSLLPPAYNKPSVSLPPVLPWTEPDCDFPDEKDSYWEF

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	12.21 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.92 RPM
SRP007412_cerebellum	0.06 RPM	17.44 RPM
SRP007412_heart	0.00 RPM	28.38 RPM
SRP007412_kidney	0.35 RPM	128.64 RPM
SRP007412_liver	0.24 RPM	70.14 RPM
SRP007412_testis	0.19 RPM	9.20 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1741 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1741 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1741 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3920
Gorilla gorilla	retro_ggor_2638
Pongo abelii	retro_pabe_3192

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000082146	2 retrocopies	retro_hsap_147, retro_hsap_3920,
Gorilla gorilla	ENSGGOG00000012183	1 retrocopy	retro_ggor_2638,
Macaca mulatta	ENSMMUG00000018141	1 retrocopy	retro_mmul_1741 ,
Nomascus leucogenys	ENSNLEG00000006967	1 retrocopy	retro_nleu_2158,
Otolemur garnettii	ENSOGAG00000010744	1 retrocopy	retro_ogar_1019,
Pongo abelii	ENSPPYG00000013074	1 retrocopy	retro_pabe_3192,