RetrogeneDB ID: retro_mmul_2550

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:6382454..6383310(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000014224
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DRAXIN
• Ensembl ID: ENSMMUG00000001652
• Aliases: DRAXIN, C1H1orf187
• Description: dorsal inhibitory axon guidance protein [Source:HGNC Symbol;Acc:25054]

Sequence

>retro_mmul_2550
CCCTCCGCCTCCTCCCTGGCGGCCCTAGTCCTAGTCCTCCTGCTGCCCCTGGAGCTGAGCCTGGCAAATGCCCTTGCACC
TGGGACTCCTGCTCAGAATCTCCCCGAGAATCACATCGACCTCCCTGGCCCAGCACTGTGGTCGCCTCAGGCCAGCCACC
ACTGCCAGCACGGCCCAGGCAAGAAGGAGTGGGGCTCACGCCTGCCCAGGGAGGCCCAGGATGGGGCTGTGGTCACCGCC
ACCAGGCAGGCTTCCAGACTGCCAGGGTCTGAGGGGCCGCTGCCTGAGCAGAGTCCTGCAGGCCTGCTGCGGGTGAAGGA
CCTGCTCCTGGGGCTCGAGTTGCCCTACCCCAAGAAGCAGAATCGGTCTTCAGGGTGGGAGAGGGCCAGGAAACGCAGCA
GGGAGCACAAAAGACGCAGGGACAGGCTGAGGCTGCACCGAGGCCGAGCCTTGGTCCGAGGTCCCAGCTCCCTGATGAAG
GCGGAGCTCTCCGAAGCCAAGGAGCTGGATGCGGCCATGGAGCAATCTTCCGCCAGTCGGTTCCCCACCATGATCTTCCT
CACCACCTTTGAGGCAGCATCTGCCACAGAAGAGTCCCTGATCCTGCCCATCACCTCCCTGCGGCCCCAGGCACAGCGCA
GGCCTGACGGGGAGGTGATACCCACGTTGGACATGGCCTTGTTCGACTGCACCGATTATGAAGACTTAAAACCTGATGGT
GGGCCCTCTGCAAAGAAGAAAGAAAAACCAGGGTAAACTCTCCAGTGACAGTAACGAAACATCATCAGCCGAAGCGGAAC
CGTGCGACCATCACCAAGACTGCCTGGCAGGGCTGCGCTGCTATGCCAGATTCCAC

Alignment

ORF - retro_mmul_2550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.2 %
• Parental protein coverage: 82.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PATHTAPMLFLVLLLPLELSLAGALAPGTPARNLPENHIDLPGPALWTPQASHHRRRGLGKKEWGPGLPS
          P.......L.LVLLLPLELSLA.ALAPGTPA.NLPENHIDLPGPALW.PQASHH...G.GKKEWG..LP.
Retrocopy PSASSLAALVLVLLLPLELSLANALAPGTPAQNLPENHIDLPGPALWSPQASHHCQHGPGKKEWGSRLPR

Parental  QAQDGAVVTATRQASRLPEAEGPLPEQSPAGLLQDKDLLLGLAVPYPEKENRPPGWERARKRSREHKRRR
          .AQDGAVVTATRQASRLP..EGPLPEQSPAGLL..KDLLLGL..PYP.K.NR..GWERARKRSREHKRRR
Retrocopy EAQDGAVVTATRQASRLPGSEGPLPEQSPAGLLRVKDLLLGLELPYPKKQNRSSGWERARKRSREHKRRR

Parental  DRLRLHRGRALVRGPSSLMKKAELSEAQALDAAMEESSTSLAPTMFFLTTFEAAPATEESLILPVTSLQP
          DRLRLHRGRALVRGPSSLMK.AELSEA..LDAAME.SS.S..PTM.FLTTFEAA.ATEESLILP.TSL.P
Retrocopy DRLRLHRGRALVRGPSSLMK-AELSEAKELDAAMEQSSASRFPTMIFLTTFEAASATEESLILPITSLRP

Parental  QAQPRPDGEVMPTLDMALFDWTDYEDLKPDG-WPSAK-KKEKHRGKLSSDGNETSPVEGEPCDHHQDCLP
          QAQ.RPDGEV.PTLDMALFD.TDYEDLKPDG.W...K....K..GKLSSD.NETS..E.EPCDHHQDCL.
Retrocopy QAQRRPDGEVIPTLDMALFDCTDYEDLKPDG<WALCK<RRKKNQGKLSSDSNETSSAEAEPCDHHQDCLA

Parental  GTCCDLREH
          G..C..R.H
Retrocopy GLRCYARFH

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	0.11 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.16 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.23 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2550 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2550 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2550 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4779
Pongo abelii	retro_pabe_3719

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000162490	1 retrocopy	retro_hsap_4779,
Macaca mulatta	ENSMMUG00000001652	1 retrocopy	retro_mmul_2550 ,
Pongo abelii	ENSPPYG00000001884	1 retrocopy	retro_pabe_3719,
Pan troglodytes	ENSPTRG00000000150	1 retrocopy	retro_ptro_3065,