RetrogeneDB ID: retro_ptro_1475

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:25313529..25314102(-)
• Located in intron of: ENSPTRG00000013912

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL21A
• Ensembl ID: ENSPTRG00000012852
• Aliases: METTL21A, FAM119A
• Description: methyltransferase like 21A [Source:HGNC Symbol;Acc:30476]

Sequence

>retro_ptro_1475
TTGGCCCTGTTTCCCTATGAGGAGACCCTGGGATTGGGGTTGCAGAAATTCCATAAGCCTCTTGCCACCTTTGTGAACCA
CGTGACACAGATCCGGCAGGACCGGAGACAACTGGGAATTGCCACAGTGGTTTGGGATGTGGCCATGGTTCTCTCCACAC
ATCTGGAGATGGGAGCTGTGGAGCTCTTAGGCTGCCCCGCAGTGAAACTGGGTGCTGGCATAGGGCTGATGGGCATAGTG
GCTGCCCTGCTGGGTGCTCATGTGACTGTCATAGATCGAAAAGTAGCATTAGAGTTTTGTAAATCAAATGTTCAAGGCAA
TTTACCTCCTTGTATCCAATCCAGAGCTTTTGTTAAGGAGCCGACTTGGGGAAAGAATTTGGGGAGTTTTTCTCCTAGAG
ATTTTGACCTGATACTTGGAGCCGATATCATATATTTAGAAGAAACATTCACAGATCTTCTTCAAACACTGGACCATCTC
TGTAGCAATCACTCCATGATTCTTTTACCTTGCTTAATTCACTATGAACGGAGTAACTTTTGAGCAATGCTGGAGAGGCA
GTTTACTGTAAGG

Alignment

ORF - retro_ptro_1475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.32 %
• Parental protein coverage: 88.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALVPYEETTEFGLQKFHKPLATFSFANHTIQIRQDWRHLGVAAVVWDAAIVLSTYLEMGAVELRGRSAV
          .AL.PYEET...GLQKFHKPLATF...NH..QIRQD.R.LG.A.VVWD.A.VLST.LEMGAVEL.G..AV
Retrocopy LALFPYEETLGLGLQKFHKPLATF--VNHVTQIRQDRRQLGIATVVWDVAMVLSTHLEMGAVELLGCPAV

Parental  ELGAGTGLVGIVAALLGAHVTITDRKVALEFLKSNVQANLPPHIQPKTVVKELTWGQNLGSFSPGEFDLI
          .LGAG.GL.GIVAALLGAHVT..DRKVALEF.KSNVQ.NLPP.IQ....VKE.TWG.NLGSFSP..FDLI
Retrocopy KLGAGIGLMGIVAALLGAHVTVIDRKVALEFCKSNVQGNLPPCIQSRAFVKEPTWGKNLGSFSPRDFDLI

Parental  LGADIIYLEETFTDLLQTLEHLCSNHSVILLACRIRYERDNNFLAMLERQFTVR
          LGADIIYLEETFTDLLQTL.HLCSNHS.ILL.C.I.YER..NF.AMLERQFTVR
Retrocopy LGADIIYLEETFTDLLQTLDHLCSNHSMILLPCLIHYER-SNF*AMLERQFTVR

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	0.02 RPM	4.27 RPM
SRP007412_cerebellum	0.07 RPM	5.92 RPM
SRP007412_heart	0.03 RPM	4.26 RPM
SRP007412_kidney	0.05 RPM	6.38 RPM
SRP007412_liver	0.00 RPM	6.19 RPM
SRP007412_testis	0.00 RPM	22.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1475 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1475 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2532
Pongo abelii	retro_pabe_1863
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	ENSPPYG00000013116	1 retrocopy	retro_pabe_1863,
Pan troglodytes	ENSPTRG00000006327	1 retrocopy	retro_ptro_286,
Pan troglodytes	ENSPTRG00000012852	1 retrocopy	retro_ptro_1475 ,