RetrogeneDB ID: retro_mmul_1608

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:60709619..60710324(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPZL1
• Ensembl ID: ENSMMUG00000009184
• Aliases: None
• Description: None

Sequence

>retro_mmul_1608
TTGACAGCTGGAGTACCAGCCTTGGAAGCATATACACCAAAAGAAATCTTCATGGCAAATGGTACATAAGGGAAGCTGAC
CTGCAAGCTCAAGTCTACTAATATGACTGGCGGGTTGACCTCAGTCTTCTGAAGCTTCCAGCCAGAGGGGGCTGACACCA
CCACGTCATTTTTCCACTATTCCCAAGGGCAGGTGTACCTTGGGAATTATCCACTATTTAAAGACAGAATCAGCTGGGCT
GAAGACCTTGACAAGAAAGATGCATCAATCAACACAGAAAATATGCAGTCTATATACAATGGCACCTATAGCTGTGATGT
CAAAAACCCTCCTGACATTGTTTTCCAGTCTGGACACATTAGGCTCTATGTTGTAGAAAAAGAGAGGTTGCCTGTGTTTC
CAGTTTGGGTAGTGTGGGGCATAGTTACTACTGTGATCCTAGGTCTCACTCTGCTCATCAGCATGATTCTGGCTGTCCTC
TATAGAAGGAAAAACTCTAAACGGGGTTACATCAGAGAGTTTGTCACACCAGTTAAACAGGCTCCTCGGAAGTCCCACTC
TGACACTGAGGGTTTTGTAAAGAGACTGCCTTCTGGATCTCACCAGGTCCCAGTCATATATGCACAGTTAGACCACTCTG
GTGGACATCACAGTGACAAGATTAACAAGTCAGAGTCTGTGGTGTATGCGGATATCTGAAAAAAT

Alignment

ORF - retro_mmul_1608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTAGVSALEVYTPKEIFVANGTQGKLTCKFKSTDETGGLTSVTWSFQPEGADTTVSFFHYSQGQVYPGNY
          .TAGV.ALE.YTPKEIF.ANGT.GKLTCK.KST..TGGLTSV..SFQPEGADTT.SFFHYSQGQVY.GNY
Retrocopy LTAGVPALEAYTPKEIFMANGT*GKLTCKLKSTNMTGGLTSVF*SFQPEGADTTTSFFHYSQGQVYLGNY

Parental  PPFKDRISWAGDLDKKDASINIENMQFIHNGTYICDVKNPPDIVVQPGHIRLYVVEKENLPVFPVWVVVG
          P.FKDRISWA.DLDKKDASIN.ENMQ.I.NGTY.CDVKNPPDIV.Q.GHIRLYVVEKE.LPVFPVWVV.G
Retrocopy PLFKDRISWAEDLDKKDASINTENMQSIYNGTYSCDVKNPPDIVFQSGHIRLYVVEKERLPVFPVWVVWG

Parental  IVTAVVLGLTLLISMILAVLYRRKNSKRDYTGCSTSESLSPVKQAPRKSPSDTEGLVKSLPSGSHQGPVI
          .....V....L.........................E...PVKQAPRKS.SDTEG.VK.LPSGSHQ.PVI
Retrocopy ----IVTTVILGLTLLISMILAVLYRRKNSKRGYIREFVTPVKQAPRKSHSDTEGFVKRLPSGSHQVPVI

Parental  YAQLDHSGGHHSDKINKSESVVYADIRKN
          YAQLDHSGGHHSDKINKSESVVYADI.KN
Retrocopy YAQLDHSGGHHSDKINKSESVVYADI*KN

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	13.78 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	12.53 RPM
SRP007412_cerebellum	0.13 RPM	12.98 RPM
SRP007412_heart	0.00 RPM	7.83 RPM
SRP007412_kidney	0.00 RPM	6.81 RPM
SRP007412_liver	0.00 RPM	4.91 RPM
SRP007412_testis	0.00 RPM	6.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1608 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1608 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1608 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000197965	1 retrocopy	retro_hsap_3859,
Macaca mulatta	ENSMMUG00000009184	1 retrocopy	retro_mmul_1608 ,
Pongo abelii	ENSPPYG00000000548	1 retrocopy	retro_pabe_3048,
Pan troglodytes	ENSPTRG00000024131	1 retrocopy	retro_ptro_2630,