RetrogeneDB ID: retro_pabe_1863

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:40307748..40308372(-)
• Located in intron of: ENSPPYG00000011424

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL21A
• Ensembl ID: ENSPPYG00000013116
• Aliases: None
• Description: Methyltransferase-like protein 21A [Source:UniProtKB/Swiss-Prot;Acc:Q5RE14]

Sequence

>retro_pabe_1863
TTGGCCCTGTTGCCCTATGAGGAGACCGTGGGATTGGGGTTGCAGAAATTCCACAAGCCTCTTGCCACCTTTGTGAACCA
CATGACACAGATCCGGCAGGACCGGAGACAACTGGGAATTGCCTCAGTGGTTTGGGATGTGGCCATGGTTCTCTCCACAC
ATCTGGAGATGGGAGCTGTGGAGCTCTTGGGCTGCCCCGCAGTGAAACTGGGTGCTGGCTTAGGGCTGATGGGCATAGTG
GCTGCCCTGCTGGGTGCTCATGTGAGTATCACAGATCAAAAAGTAGCATTAGAGTTTTGTAAATCAAATGTTCAAGGCAG
TTTACCTCCTTGTATCCAGCCCAGAGCTTTTGTTAAGGAGCTGACTTGGGGAAAGAATTTGGGGAGTTTTTCTCCTAGAG
ATTTTGACCTGATACTTGGAGCCGATATCATATATTTAGAAGAAACATTCACAGATCTTCTTCAAACACTGTACCATCTC
TGTAGCAATCACTCCATGATTCTTTTACCTTGCTGAATTCACGATGAACGGAGTAACTTTTGAGCAATGCTGGAGAGGCA
GTTTAAGGTTCACTATGATACTGAGAAAGATGTACTTATGTATACAGAAGAGAAGCCACAGCAG

Alignment

ORF - retro_pabe_1863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.83 %
• Parental protein coverage: 98.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALVPYEETTEFGLQKFHKPLKTFSFANHTIQIRQDWRHLGVAAVVWDAAIVLSTYLEMGAVELRGRSAV
          .AL.PYEET...GLQKFHKPL.TF...NH..QIRQD.R.LG.A.VVWD.A.VLST.LEMGAVEL.G..AV
Retrocopy LALLPYEETVGLGLQKFHKPLATF--VNHMTQIRQDRRQLGIASVVWDVAMVLSTHLEMGAVELLGCPAV

Parental  ELGAGTGLVGIVAALLGAHVTITDRKVALEFLKSNVQANLPPHIQPKTVVKELTWGQNLGSFSPGEFDLI
          .LGAG.GL.GIVAALLGAHV.ITD.KVALEF.KSNVQ..LPP.IQP...VKELTWG.NLGSFSP..FDLI
Retrocopy KLGAGLGLMGIVAALLGAHVSITDQKVALEFCKSNVQGSLPPCIQPRAFVKELTWGKNLGSFSPRDFDLI

Parental  LGADIIYLEETFTDLLQTLEHLCSNHSVILLACRIRYERDNNFLAMLERQFTVRKVHYDPEKDVHIYEAQ
          LGADIIYLEETFTDLLQTL.HLCSNHS.ILL.C.I..ER..NF.AMLERQF...KVHYD.EKDV..Y...
Retrocopy LGADIIYLEETFTDLLQTLYHLCSNHSMILLPC*IHDER-SNF*AMLERQF---KVHYDTEKDVLMYTEE

Parental  KRNQ
          K..Q
Retrocopy KPQQ

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	9.01 RPM
SRP007412_cerebellum	0.12 RPM	6.81 RPM
SRP007412_heart	0.15 RPM	3.91 RPM
SRP007412_kidney	0.00 RPM	7.79 RPM
SRP007412_liver	0.03 RPM	6.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1863 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1863 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2532
Pan troglodytes	retro_ptro_1475
Macaca mulatta	retro_mmul_1594

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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	ENSG00000144401	1 retrocopy	retro_hsap_2532,
Macaca mulatta	ENSMMUG00000022602	1 retrocopy	retro_mmul_1594,
Nomascus leucogenys	ENSNLEG00000007129	2 retrocopies	retro_nleu_2926, retro_nleu_471,
Pongo abelii	ENSPPYG00000005798	1 retrocopy	retro_pabe_337,
Pongo abelii	ENSPPYG00000013116	1 retrocopy	retro_pabe_1863 ,
Pan troglodytes	ENSPTRG00000012852	1 retrocopy	retro_ptro_1475,