RetrogeneDB ID: retro_mmul_2336

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:43824108..43824721(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB4A
• Ensembl ID: ENSMMUG00000017720
• Aliases: None
• Description: ras-related protein Rab-4A [Source:RefSeq peptide;Acc:NP_001244480]

Sequence

>retro_mmul_2336
AAGTTCTTAGTTATTGGAAATGCAGAACTGGCAAATCTTGCTTATTTCGTCAGTTTATTGGAAAAAAAAAATCAAAATGA
TTCAAATCATACAATAGGAGTGGAATTTGGTTCAAAGGTAATAAATGTTTGTGGTAAATATGTAAAGTTACAAATACGGG
ATACAGCACGACAAGAATGATTCAAGTCTGTGAAGAGAAGTTATTACCCAGGGGCGACCGGGGCTCTCCTCGTCTATAAT
ATCAGCAGCCGAGAAACCTACAATGCACTTACTAATTGGTTAACAGATGCCCGAATGCTAGCGAGTCAGAACATTGTGAT
CATCCTTTGTGGAAACAAGAAGGACCTGGATGCAGATCGTGAAGTTACCTTCTTAGAAGCCTCCCGATTTGCTCAAGAAA
ATTAGCTGATGTTTTTGGAAACAAGTGCACTAACAGGGGAGAATGTAGAAGAGGCTTTTGTACAGTGTGCAAGAAAAAAT
ACTTAACAAAATTGAATCAGATGAGCTGGACCCAGAAAGAATGGGCTCAGGTGTTCAGTACAGAGATGCTGTATTGAGAC
AGCTGAAATCACTGCGGTGCACACAGGCCCCAAAAGCTCAGGAGTGTGGTTGT

Alignment

ORF - retro_mmul_2336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.06 %
• Parental protein coverage: 93.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KFLVIGNAG-TGKSCLLHQFIEKKF-KDDSNHTIGVEFGSKIINVGGKYVKLQIWDTAGQERFRSVTRSY
          KFLVIGNA..TGKSCL..QFI.......DSNHTIGVEFGSK.INV.GKYVKLQI.DTA.QE.F.SV.RSY
Retrocopy KFLVIGNAE<TGKSCLFRQFIXXXX>QNDSNHTIGVEFGSKVINVCGKYVKLQIRDTARQE*FKSVKRSY

Parental  YRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDLDADREVTFLEASRFAQENELMF
          Y.GA.GALLVY.I.SRETYNALTNWLTDARMLASQNIVIILCGNKKDLDADREVTFLEASRFAQEN.LMF
Retrocopy YPGATGALLVYNISSRETYNALTNWLTDARMLASQNIVIILCGNKKDLDADREVTFLEASRFAQEN*LMF

Parental  LETSALTGENVEEAFVQCAR-KILNKIESGELDPERMGSGIQYGDAALRQLRSPRRAQAPNAQECGC
          LETSALTGENVEEAFVQCAR.KILNKIES.ELDPERMGSG.QY.DA.LRQL.S.R..QAP.AQECGC
Retrocopy LETSALTGENVEEAFVQCAR>KILNKIESDELDPERMGSGVQYRDAVLRQLKSLRCTQAPKAQECGC

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	31.04 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	30.70 RPM
SRP007412_cerebellum	0.13 RPM	22.54 RPM
SRP007412_heart	0.00 RPM	21.79 RPM
SRP007412_kidney	0.00 RPM	17.25 RPM
SRP007412_liver	0.00 RPM	11.52 RPM
SRP007412_testis	0.00 RPM	33.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2336 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2336 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013866	5 retrocopies	retro_chof_1017, retro_chof_1761, retro_chof_2377, retro_chof_64, retro_chof_703,
Echinops telfairi	ENSETEG00000018042	3 retrocopies	retro_etel_1163, retro_etel_122, retro_etel_681,
Macaca mulatta	ENSMMUG00000008006	1 retrocopy	retro_mmul_2463,
Macaca mulatta	ENSMMUG00000017720	1 retrocopy	retro_mmul_2336 ,
Nomascus leucogenys	ENSNLEG00000014339	1 retrocopy	retro_nleu_2062,
Pongo abelii	ENSPPYG00000000128	1 retrocopy	retro_pabe_3321,