RetrogeneDB ID: retro_pabe_3048

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:22745420..22746224(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPZL1
• Ensembl ID: ENSPPYG00000000548
• Aliases: None
• Description: myelin protein zero-like 1 [Source:HGNC Symbol;Acc:7226]

Sequence

>retro_pabe_3048
ATGGCAGCGCCCACCAGAGCCGGGGCAGTGATTACAGCCCCAGACAGGAGGCGCTGGCTGTGGTTGGTTCTGGTGGTGGC
GCTGGGGCTCTTGACAGCTGGAGTATCAGCCTTGGAAGTATATTTACCAAAAGAAATCTTCGTGGCAAATGGTACACAAG
GGAAGCTGACCTGCAAGTTCAAGTCTACTAATACGACTGGCGGGTTGACCTCAGTCTCCTGGAGCTTCCAGCCAGAGGAG
GCCGACACCACCGTGTGATTTTGCCACTACTCCCAAGGGCAAGTGTACCTTGGGAATTATCCACCATTTAGATACAGAAT
CAGCTGGGCTGGAGACATTGACAAGAAAGATGCATCAATCAACATAGAAAATATGCAGTTTATACACAATGGCACCTATA
TCTGTGATGTCAAAAACCCTCCTGACATTGTTGTCCAGCCTGGACACATTAGGCTCTGTGTCATAGAGAAAGAGAGTTTG
CCTGTGTTTCCAGTTTGGGTAGTGGTGGGCATAGTTACTGCTGTGGTCCTAGGTCTCACTCTGCTCATCAGCATGATTCT
GGCTGTCCTCTATAGAAGGAAAAACTCTAAACAGGATTAAACTGGCTGCAGTACATCAGAGAGTTTGTTACCAGTTAAGT
AGGCTCCTCAGAAGTCCCCCTCTGACACTGAGGGTCTTGTAAAGAGTCTGCCTTCTGGATCTCACCAGGGCCCAGTCATA
TATGCACAGTTAGACCACTCTAGTGGACATCAGAGTGACAAGATTAACAAGTCAGTCTGTGGTGTATGTGGATATCTGAA
AAAA

Alignment

ORF - retro_pabe_3048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.69 %
• Parental protein coverage: 99.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPAEAGAVIAAPDSRRWLWSVLAAALGLLTAGVSALEVYTPKEIFVANGTQGKLTCKFKSTSTTGGLT
          MAAP..AGAVI.APD.RRWLW.VL..ALGLLTAGVSALEVY.PKEIFVANGTQGKLTCKFKST.TTGGLT
Retrocopy MAAPTRAGAVITAPDRRRWLWLVLVVALGLLTAGVSALEVYLPKEIFVANGTQGKLTCKFKSTNTTGGLT

Parental  SVSWSFQPEGADTTVSFFHYSQGQVYLGNYPPFKDRISWAGDLDKKDASINIENMQFIHNGTYICDVKNP
          SVSWSFQPE.ADTTV.F.HYSQGQVYLGNYPPF..RISWAGD.DKKDASINIENMQFIHNGTYICDVKNP
Retrocopy SVSWSFQPEEADTTV*FCHYSQGQVYLGNYPPFRYRISWAGDIDKKDASINIENMQFIHNGTYICDVKNP

Parental  PDIVVQPGHIRLYVVEKENLPVFPVWVVVGIVTAVVLGLTLLISMILAVLYRRKNSKRDYTGCSTSESLS
          PDIVVQPGHIRL.V.EKE.LPVFPVWVVVGIVTAVVLGLTLLISMILAVLYRRKNSK.D.TGCSTSESL.
Retrocopy PDIVVQPGHIRLCVIEKESLPVFPVWVVVGIVTAVVLGLTLLISMILAVLYRRKNSKQD*TGCSTSESLL

Parental  PVKQAPRKSPSDTEGLVKSLPSGSHQGPVIYAQLDHSGGHHSDKINKSESVVYADIRK
          PVK.AP.KSPSDTEGLVKSLPSGSHQGPVIYAQLDHS.GH.SDKINKS...V.....K
Retrocopy PVK*APQKSPSDTEGLVKSLPSGSHQGPVIYAQLDHSSGHQSDKINKSVCGVCGYLKK

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_prefrontal_cortex	0.00 RPM	26.43 RPM
SRP007412_cerebellum	0.00 RPM	35.14 RPM
SRP007412_heart	0.00 RPM	21.79 RPM
SRP007412_kidney	0.03 RPM	58.37 RPM
SRP007412_liver	0.00 RPM	28.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3048 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3048 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3048 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2630

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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	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,