RetrogeneDB ID: retro_mmul_1648

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:173166843..173167238(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1995
• Ensembl ID: ENSMMUG00000004341
• Aliases: None
• Description: protein max [Source:RefSeq peptide;Acc:NP_001248298]

Sequence

>retro_mmul_1648
CATCATGATGCACTGGAATGAAATCGTAGGGACCACATCAAAGGCAGCTTTCAGTTTGTGGGACTCAGTCCCAATACTCC
AAGGAGAGAAGGCATCCGGGGCCCAAATCCTAGACAAAGCCATAGAGTATATCCAGCATATGTGGAGGGAAAAACCACAC
GCCAGTGAGAAATCGATGACCTCAGCGGTAGAATGCTCTTCTGAAGCAGGAAGTCCGTGCACTGAAGGGGAGGTCAAGTG
CCCAGCCACAGGCCAACTATCCCTCCTCAGACAGCATCCTCTACACCAATGCCAAGGGCAGCACCACCTCTGCCTTTGAT
GGGGGCTCCGACTCCAGCTCAGAGTTGGAGCATGAAGAGCCCTGAAGTAGGAAGAAACTCCAGATGGAGGCCAGC

Alignment

ORF - retro_mmul_1648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.72 %
• Parental protein coverage: 83.75 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HHNALERKRRDHI-KDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNH-THQQDIDDL-KRQNA
          HH.ALE..RRDHI.K..F.SL.DSVP.LQGEKAS.AQILDKA.EYIQ.M.R....T.Q..IDDL..R.NA
Retrocopy HHDALE*NRRDHI>KAAF-SLWDSVPILQGEKASGAQILDKAIEYIQHMWREKP<TRQ*EIDDL<QR*NA

Parental  LLEQQVRALEKARSSAQLQTNYPSSDNSLYTNAKGSTISAFDGGSDSSSESEPEEPQSRKKLRMEAS
          LL.Q.VRAL.K.RSSAQ.Q.NYPSSD..LYTNAKGST.SAFDGGSDSSSE.E.EEP.SRKKL.MEAS
Retrocopy LLKQEVRAL-KGRSSAQPQANYPSSDSILYTNAKGSTTSAFDGGSDSSSELEHEEP*SRKKLQMEAS

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	0.22 RPM	38.32 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	37.92 RPM
SRP007412_cerebellum	0.32 RPM	57.60 RPM
SRP007412_heart	0.00 RPM	25.20 RPM
SRP007412_kidney	0.00 RPM	30.05 RPM
SRP007412_liver	0.00 RPM	15.75 RPM
SRP007412_testis	0.11 RPM	23.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1648 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1648 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3097

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003472	2 retrocopies	retro_amel_1261, retro_amel_1606,
Canis familiaris	ENSCAFG00000016212	2 retrocopies	retro_cfam_1179, retro_cfam_1325,
Callithrix jacchus	ENSCJAG00000019702	2 retrocopies	retro_cjac_2057, retro_cjac_2556,
Cavia porcellus	ENSCPOG00000010172	1 retrocopy	retro_cpor_710,
Erinaceus europaeus	ENSEEUG00000003973	3 retrocopies	retro_eeur_216, retro_eeur_344, retro_eeur_37,
Echinops telfairi	ENSETEG00000002967	1 retrocopy	retro_etel_1294,
Felis catus	ENSFCAG00000010347	1 retrocopy	retro_fcat_278,
Macaca mulatta	ENSMMUG00000004341	1 retrocopy	retro_mmul_1648 ,
Mustela putorius furo	ENSMPUG00000006859	3 retrocopies	retro_mputfur_1218, retro_mputfur_1615, retro_mputfur_192,
Mus musculus	ENSMUSG00000059436	8 retrocopies	retro_mmus_2891, retro_mmus_2892, retro_mmus_2893, retro_mmus_2894, retro_mmus_2991, retro_mmus_2992, retro_mmus_2993, retro_mmus_2994,
Nomascus leucogenys	ENSNLEG00000014373	1 retrocopy	retro_nleu_1122,
Ochotona princeps	ENSOPRG00000016245	1 retrocopy	retro_opri_945,
Pongo abelii	ENSPPYG00000005911	1 retrocopy	retro_pabe_3097,
Rattus norvegicus	ENSRNOG00000008049	3 retrocopies	retro_rnor_1653, retro_rnor_1877, retro_rnor_2369,
Ictidomys tridecemlineatus	ENSSTOG00000028142	1 retrocopy	retro_itri_42,
Tupaia belangeri	ENSTBEG00000012645	1 retrocopy	retro_tbel_3407,