RetrogeneDB ID: retro_ptro_286

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:38016845..38017205(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042294
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: METTL21D
• Ensembl ID: ENSPTRG00000006327
• Aliases: None
• Description: methyltransferase like 21D [Source:HGNC Symbol;Acc:20352]

Sequence

>retro_ptro_286
ATGAGCAAGCATCTTGTCACTGGTTCTGTTCAAGCCAAGGTACTGAAATGGGGGGAAGAAATAGAAGACTTTCCTCCTCC
ACCCGTCTACATACTGATGGCCGACTGCATATACTATGAAGAGTCTTTGGAGCCATTGCTGAAAACTCTAAAAGATATCA
GTGGATTTGAGAGTTGTATAATATGTTGTTATGAACAACAAAGAATGGGAAAAAGTCCAGATATTGAGAAAAAATACTTT
GAGCTCCTTCAGCTAGACTTTGACTTTGAAAAAATTCCTTTGGAAAAACATGATGAAGAGTACCAAAGTGAAGATATTCA
TATTATATACATCAGAAAGAAAAAATGGAAATTTTCATCA

Alignment

ORF - retro_ptro_286 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 52.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNKHLVTGSVQAKVLKWGEEIEGFPSPPDYILMADCIYYEESLEPLLKTLKDISGFETCIICCYEQRTMG
          M.KHLVTGSVQAKVLKWGEEIE.FP.PP.YILMADCIYYEESLEPLLKTLKDISGFE.CIICCYEQ..MG
Retrocopy MSKHLVTGSVQAKVLKWGEEIEDFPPPPVYILMADCIYYEESLEPLLKTLKDISGFESCIICCYEQQRMG

Parental  KNPEIEKKYFELLQLDFDFEKIPLEKHDEEYRSEDIHIIYIRKKKSKFPS
          K.P.IEKKYFELLQLDFDFEKIPLEKHDEEY.SEDIHIIYIRKKK.KF.S
Retrocopy KSPDIEKKYFELLQLDFDFEKIPLEKHDEEYQSEDIHIIYIRKKKWKFSS

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	0.04 RPM	7.33 RPM
SRP007412_cerebellum	0.04 RPM	6.13 RPM
SRP007412_heart	0.00 RPM	2.04 RPM
SRP007412_kidney	0.00 RPM	3.64 RPM
SRP007412_liver	0.00 RPM	2.00 RPM
SRP007412_testis	0.00 RPM	4.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_286 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_286 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_286 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_365
Pongo abelii	retro_pabe_337

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013492	1 retrocopy	retro_dnov_1734,
Homo sapiens	ENSG00000100483	1 retrocopy	retro_hsap_365,
Mustela putorius furo	ENSMPUG00000004994	1 retrocopy	retro_mputfur_886,
Pongo abelii	ENSPPYG00000005798	1 retrocopy	retro_pabe_337,
Pan troglodytes	ENSPTRG00000006327	1 retrocopy	retro_ptro_286 ,
Pan troglodytes	ENSPTRG00000012852	1 retrocopy	retro_ptro_1475,