RetrogeneDB ID: retro_pabe_3557

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:104054..104725(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPPE1
• Ensembl ID: ENSPPYG00000008997
• Aliases: None
• Description: metallophosphoesterase 1 [Source:RefSeq peptide;Acc:NP_001124783]

Sequence

>retro_pabe_3557
ATGGCTATGAGTGGATTGAGGTTTGGAAGACAGAATTTTCATCCGTTGAAGAGGAAGAGTTGATTGCTGTTGAAATTCAT
TGTCTTTCCTGTGCTTCTGTTTTGTGAATTTTTAATTTATTACTTAGTGATCTTTTGGTGTAACTGGCCTGAAGTGAAAA
CCGCAGCCTATGATGGTGAACAGGCCACGTGTGAACCTGTGCTCAAAGTCATGTTTTTTGCTGACACCCACTTGCCTGGG
GAATTCCTAGGTCACTGGCTGGACAAATTACGAAGGGAATGGCAGGTGGAGAGAGCCTTCCAGACAGCTCTGTGGTTGCT
GCAGCCGGAAGTCGTCTTCATCCTGGAGGATGTCTTTGATGAAGGGAAGTGGAGCACCCCTGAGGCCTGGGTGGATGACG
TGGAGCAGTTTCAGAAAATGTTCAGTTACCCAAGTCACGTGCAGCTGAAGGTAGTTGCTGGAAACCATGACACTGGCTTC
CACTATGAGGTGAACACATACGAAGTAGAACGGTTTGAGAAAGTGTTCATCTCTGAAAGCCTGTTTTCTTGGAAAGGATT
AACTTCGTGATGGTCAACAGCATGGCACTGAAGGGGGACAGCTGTGGCATCTGTTCTGAAGCAGAAGCAGAGCTCATTGA
AGTTTCTTACAGACTGAATTTCTCCCGAGAG

Alignment

ORF - retro_pabe_3557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.7 %
• Parental protein coverage: 57.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMIELEFGRQNFHPLKKKSPLLLKLIAVVFAVLLFCEFLIYYLAIFQCNWPEVKTTASDGEQATREPVL
          MAM..L.FGRQNFHPLK.KS.LLLK.I..VF.VLLFCEFLIYYL.IF.CNWPEVKT.A.DGEQAT.EPVL
Retrocopy MAMSGLRFGRQNFHPLKRKS*LLLKFI--VFPVLLFCEFLIYYLVIFWCNWPEVKTAAYDGEQATCEPVL

Parental  KAMFLADTHLLGEVLGHWLDKLRREWQMERAFQTALWLLQPEVVFILGDIFDEGKWSTPEAWVNDVERFQ
          K.MF.ADTHL.GE.LGHWLDKLRREWQ.ERAFQTALWLLQPEVVFIL.D.FDEGKWSTPEAWV.DVE.FQ
Retrocopy KVMFFADTHLPGEFLGHWLDKLRREWQVERAFQTALWLLQPEVVFILEDVFDEGKWSTPEAWVDDVEQFQ

Parental  KMFRHPSHVQLKVVAGNHDIGFHYEMNTYKVERFEKVFSSERLFSWKG-INFVMVNSVALNGDGCGICSE
          KMF..PSHVQLKVVAGNHD.GFHYE.NTY.VERFEKVF.SE.LFSWKG.INFVMVNS.AL.GD.CGICSE
Retrocopy KMFSYPSHVQLKVVAGNHDTGFHYEVNTYEVERFEKVFISESLFSWKG<INFVMVNSMALKGDSCGICSE

Parental  TEAELIEVSHRLNCSRE
          .EAELIEVS.RLN.SRE
Retrocopy AEAELIEVSYRLNFSRE

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	36.77 RPM
SRP007412_cerebellum	0.00 RPM	18.60 RPM
SRP007412_heart	0.00 RPM	4.49 RPM
SRP007412_kidney	0.00 RPM	16.64 RPM
SRP007412_liver	0.00 RPM	11.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3557 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3557 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1450
Pan troglodytes	retro_ptro_986

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000154889	1 retrocopy	retro_hsap_1450,
Macaca mulatta	ENSMMUG00000011467	1 retrocopy	retro_mmul_2270,
Mus musculus	ENSMUSG00000062526	1 retrocopy	retro_mmus_869,
Otolemur garnettii	ENSOGAG00000007068	2 retrocopies	retro_ogar_1163, retro_ogar_2826,
Pongo abelii	ENSPPYG00000008997	1 retrocopy	retro_pabe_3557 ,
Pan troglodytes	ENSPTRG00000009872	1 retrocopy	retro_ptro_986,