RetrogeneDB ID: retro_mmul_185

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:77575349..77576213(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000012603
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM122B
• Ensembl ID: ENSMMUG00000016948
• Aliases: None
• Description: None

Sequence

>retro_mmul_185
ATGGCTCAGGAGAAGATGGAGCTAGACCTGGAGCTGCCTCCGGGTACGGGCGGGAGCCCGGCGGAGGGCGGCGGCAGCGG
CGGCGGCGGGGGCCTCAGGAGGTCTAACAGCGCCCCCCTGATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCAGGCCG
AGGCGCCGAGCGCCAGGCGGAACAGCACAACGTTCCCGAGCCGCCACGGCCTGCTGCTACCGGCCTCCCCTGTCCGCATG
CACAGCAGCCGCTTGCACCAGATCAAACAAGAAGAGGGTATGGACTTGATCAACCGAGAGACGGTCCACGAACGGGAGGT
GCAGACCGCAATGCAGATAAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGTGACAACGACGTGGAGAAATCCGCCTCCC
CCAAGCGCATCGATTTCATTCCTGTGTCACCGGCACCGTCACCCACTCGGGGAATTGGGAAGCAGTGTTTTTCGCCATCC
TTGCAAAGTTTTGTAAGTAGCAACGGATTGCCTCCAAGCCCTATTCCCAGCCCAACGACCCGATTTACCACCCGGAGAAG
CCAGAGCCCCATCAATTGCATTAGACCAAGTGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGATTATCAGC
CAAAGAGATTTTTCCAGGGCATCACCAACATGCTTTCTTCTGACGTTGCACAGCTGTCAGATCCTGGTGTATGTGTATCT
TCGGATACCCTTGATGGAAACAGCAGCAGTGCCGGATCTTCTTGTAACTCACCAGCGAAAGTCAGCACTACCACCGACTC
TCCTGTGTCACCTGCCCAAGCGGCTTCTCCATTTATTCCACTAGATGAACTTTCGTCTAAGTGA

Alignment

ORF - retro_mmul_185 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.44 %
• Parental protein coverage: 61.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAPACSPRPLEPNTSYGGT-LRRSSSAPLIHGLSDLSQVFQPYTLRTRRNSTTIMSRHSLLLSSSPNRIP
          L.P.....P.E...S.GG..LRRS.SAPLIHGLSD.S.VFQ......RRNSTT..SRH.LLL..SP.R..
Retrocopy LPPGTGGSPAEGGGSGGGGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPSRHGLLLPASPVRMH

Parental  SSRLHQIKREEGLDMMNRETAHEREMQTAMQISQSWDESLSLSDSDFDKPEKLYSPKRIDFTPVSPAPSP
          SSRLHQIK.EEG.D..NRET.HERE.QTAMQIS.SW.ES.SLSD.D....EK..SPKRIDF.PVSPAPSP
Retrocopy SSRLHQIKQEEGMDLINRETVHEREVQTAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSP

Parental  TRGFGKKYF
          TRG.GK..F
Retrocopy TRGIGKQCF

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	9.86 RPM	12.33 RPM
SRP007412_brain_prefrontal_cortex	9.84 RPM	12.06 RPM
SRP007412_cerebellum	6.97 RPM	8.72 RPM
SRP007412_heart	5.18 RPM	2.94 RPM
SRP007412_kidney	5.99 RPM	5.28 RPM
SRP007412_liver	4.87 RPM	1.11 RPM
SRP007412_testis	13.80 RPM	6.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_185 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_185 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_594

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001311	1 retrocopy	retro_amel_105,
Bos taurus	ENSBTAG00000001886	1 retrocopy	retro_btau_103,
Canis familiaris	ENSCAFG00000018882	1 retrocopy	retro_cfam_181,
Callithrix jacchus	ENSCJAG00000004313	1 retrocopy	retro_cjac_594,
Cavia porcellus	ENSCPOG00000011218	1 retrocopy	retro_cpor_80,
Equus caballus	ENSECAG00000018643	1 retrocopy	retro_ecab_91,
Felis catus	ENSFCAG00000024842	1 retrocopy	retro_fcat_1575,
Myotis lucifugus	ENSMLUG00000007988	1 retrocopy	retro_mluc_382,
Macaca mulatta	ENSMMUG00000016948	1 retrocopy	retro_mmul_185 ,
Mustela putorius furo	ENSMPUG00000012690	1 retrocopy	retro_mputfur_64,
Mus musculus	ENSMUSG00000036022	1 retrocopy	retro_mmus_22,
Rattus norvegicus	ENSRNOG00000050146	1 retrocopy	retro_rnor_651,
Sus scrofa	ENSSSCG00000012685	1 retrocopy	retro_sscr_60,
Ictidomys tridecemlineatus	ENSSTOG00000006261	1 retrocopy	retro_itri_61,