RetrogeneDB ID: retro_mmul_2435

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:25841209..25841742(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9827
• Ensembl ID: ENSMMUG00000006494
• Aliases: None
• Description: None

Sequence

>retro_mmul_2435
TTTGATTGTCCAGCTTGGACTGAGTTGTACATTCACCTGACTGTGATGAAGCAACTGGTCCTGCAGCTCGAGCAGTGGGG
TTTCTGAGTCTATGGAGTTTTTTCTTGTTGATTCTCAGTTCATGGTGGAGTCATTCAAGAGTATTTCTGGCATCTTGGCA
GTCCTAAGTGCCATGCTCTCTCTAGAAATTCTACAAGTCAACATCGTGATCAAAATGTAGCTGCAGAGTAAAAAAGCTAA
AAAGGAAACTGAGAGTTTCTAGATCCAGACATGGATTCCTTATTCAATTATTCTACAAATGACTTAAGAAGCAAAACATT
CAAAAAAGTAACTAAAGCTGTATGTGGACTGATGACTGCAGCATAGTTCTCTTCTTACCTCATGATCAGTCAGATGAAGA
AAGTATGAACATTGTATTATAGCATATTGATTTTGCCATTCAATGTGGAGAAGATTCAAAATTTAAATAACTAAAGGAAC
ATGAAAATAAGTCTTGTATGTTTGATGAATATTTTCAAGGACACCAGGATGAA

Alignment

ORF - retro_mmul_2435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.31 %
• Parental protein coverage: 68.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FDCPGQIELYTHLPVMKQLVQQLEQWEFRVCGVF-LVDSQFMVESFKFISGILAALSAMISLEIPQVNIM
          FDCP...ELY.HL.VMKQLV.QLEQW.F.V.GVF.LVDSQFMVESFK.ISGILA.LSAM.SLEI.QVNI.
Retrocopy FDCPAWTELYIHLTVMKQLVLQLEQWGF*VYGVF>LVDSQFMVESFKSISGILAVLSAMLSLEILQVNIV

Parental  TKMDLLSKKAKKEIE-KFLDPDMYSLLEDSTSD-LRSKKFKKMTKAICGLIDDYSMVRFLPYDQSDEESM
          .KM.L.SKKAKKE.E..FLDPDM.SL...ST.D.L......K.....C...DD.S.V.FLP.DQSDEESM
Retrocopy IKM*LQSKKAKKETE<EFLDPDMDSLFNYSTND<LKKQNIQKSN*S-CMWTDDCSIVLFLPHDQSDEESM

Parental  NIVLQHIDFAIQYGEDLEFKEPKEREDESSSMFDEYFQECQDE
          NIVL.HIDFAIQ.GED..FK..KE.E...S.MFDEYFQ..QDE
Retrocopy NIVL*HIDFAIQCGEDSKFK*LKEHENK-SCMFDEYFQGHQDE

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	9.30 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.96 RPM
SRP007412_cerebellum	0.00 RPM	9.69 RPM
SRP007412_heart	0.00 RPM	7.77 RPM
SRP007412_kidney	0.00 RPM	9.62 RPM
SRP007412_liver	0.00 RPM	2.85 RPM
SRP007412_testis	0.00 RPM	20.69 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2435 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2435 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2435 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_652
Gorilla gorilla	retro_ggor_570
Callithrix jacchus	retro_cjac_2969

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009339	1 retrocopy	retro_cjac_2969,
Dasypus novemcinctus	ENSDNOG00000016646	1 retrocopy	retro_dnov_2095,
Homo sapiens	ENSG00000111231	1 retrocopy	retro_hsap_652,
Gorilla gorilla	ENSGGOG00000001697	1 retrocopy	retro_ggor_570,
Myotis lucifugus	ENSMLUG00000015510	1 retrocopy	retro_mluc_408,
Macaca mulatta	ENSMMUG00000006494	1 retrocopy	retro_mmul_2435 ,
Nomascus leucogenys	ENSNLEG00000002831	1 retrocopy	retro_nleu_2030,