RetrogeneDB ID: retro_pabe_3402

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:31819650..31820528(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ME2
• Ensembl ID: ENSPPYG00000009163
• Aliases: None
• Description: malic enzyme 2, NAD(+)-dependent, mitochondrial [Source:HGNC Symbol;Acc:6984]

Sequence

>retro_pabe_3402
ATGTTGTCTGGGTTAAGCGTAGTTTCCACCACTTGTATTTTGGCATGTCTACATTTACACATAAAAGAAAAAGGCAAGCC
ACTTGTGCTGAATCCAAGATTACAAACAAGGGAATGGCACTTACTTTACAAGAACGACAAATGCTTGGTCTTCAAGGGCT
TCTACCTCCCCAAATACAGACATAAGATATTCAAGCCTTATGATTCCATAGAAACTTGAAAAAAATGACTAGCCCTTCGG
AAAAATATATCTACATAATGGGAATACAAGAAAGAAATGATAAATAGTTTCATAGAATACTGCAAGATGACACTGAGAGT
TTAATGCCAATTGTATATACACCGACGGTTGGTCTTGTCTGCTCCCAGTATGGACATCTCTTTAGAAGACCTAAGGGATT
ATTTATTTCCATCTCAGACAGAGGTCATGTTAGATCAATTGTGGATAAGTGGCCAGAAAATCATGTTAAGGCTGTTTTAG
TGACTGATGGAGAGATAATTCTGGGTCTTGGAGATCTGGGTGTCTATGGAATGGGGATTGCAGTAGGAAAAATTTGTTTG
TATACAGTTTGTCCAGGAATATGGCCTGATAGATGCCTTCTGGTGTGTATTGATGTGGGAACTGATAATATCGCACTCTT
AAAAGATACATTTTACATGGGCTTGTACCAGAAACGAGATCGCACACAACAGTCTGATGATCTGATTGATGAGTTTATGA
AAGCTACTGCTGACAGATATGGCTGGAACACACTCATTCAATTTGAAGGTTTTGGAAATCATAATGCATTCAGGTTCTTG
AGAAAATACCAATAAAAATGTTGCTCTTTCAATGATGATATTCAAGGGACAGCTGCAGTAGCTCTAGTAGGTCTTCTT

Alignment

ORF - retro_pabe_3402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 53.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSRLRVVSTTCTLACRHLHIKEKGKPLMLNPR-TNKGMAFTLQERQMLGLQGLLPPK-IETQDIQALRF
          MLS.L.VVSTTC.LAC.HLHIKEKGKPL.LNPR...............L...G...PK.I.T.DIQAL.F
Retrocopy MLSGLSVVSTTCILACLHLHIKEKGKPLVLNPRLQTREWHLLYKNDKCLVFKGFYLPK<IQT*DIQAL*F

Parental  HRNLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQYGHIFRRPKGLFISIS
          HRNLKKMTSP.EKYIYIMGIQERN.K.F.RILQDD.ESLMPIVYTPTVGL.CSQYGH.FRRPKGLFISIS
Retrocopy HRNLKKMTSPSEKYIYIMGIQERNDK*FHRILQDDTESLMPIVYTPTVGLVCSQYGHLFRRPKGLFISIS

Parental  DRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTD
          DRGHVRSIVD.WPENHVKAV.VTDGE.ILGLGDLGVYGMGI.VGK.CLYT.C.GI.PDRCL.VCIDVGTD
Retrocopy DRGHVRSIVDKWPENHVKAVLVTDGEIILGLGDLGVYGMGIAVGKICLYTVCPGIWPDRCLLVCIDVGTD

Parental  NIALLKDPFYMGLYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFND
          NIALLKD.FYMGLYQKRDRTQQ.DDLIDEFMKA..DRYG.NTLIQFE.FGNHNAFRFLRKY..K.C.FND
Retrocopy NIALLKDTFYMGLYQKRDRTQQSDDLIDEFMKATADRYGWNTLIQFEGFGNHNAFRFLRKYQ*KCCSFND

Parental  DIQGIANLIVMSMV
          DIQG.A........
Retrocopy DIQGTAAVALVGLL

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	0.33 RPM	9.23 RPM
SRP007412_cerebellum	0.00 RPM	7.17 RPM
SRP007412_heart	0.69 RPM	25.65 RPM
SRP007412_kidney	0.46 RPM	13.49 RPM
SRP007412_liver	0.49 RPM	9.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3402 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3402 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4237
Gorilla gorilla	retro_ggor_2838
Callithrix jacchus	retro_cjac_615

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001929	1 retrocopy	retro_cjac_615,
Homo sapiens	ENSG00000082212	1 retrocopy	retro_hsap_4237,
Gorilla gorilla	ENSGGOG00000010823	1 retrocopy	retro_ggor_2838,
Nomascus leucogenys	ENSNLEG00000011833	1 retrocopy	retro_nleu_2307,
Pongo abelii	ENSPPYG00000009163	2 retrocopies	retro_pabe_3402 , retro_pabe_3510,