RetrogeneDB ID: retro_ptro_1822

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:130002668..130003031(+)
• Located in intron of: ENSPTRG00000015338

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL5
• Ensembl ID: ENSPTRG00000012621
• Aliases: None
• Description: methyltransferase like 5 [Source:HGNC Symbol;Acc:25006]

Sequence

>retro_ptro_1822
CACAGTGAAGCACATATGCTCTATACAATCCATAACACATGTGATGAGGTAGAAAATAAAGTGGCTGCAGATCTAGGATG
TGGCTGTGGAGTGCTTAGTCTTGGAACTGCAATGTTAGGAGCCAGGTTGTATGTTGGATTTGACATAGATGCAGGTGCAC
TAGGAATATTTAATAGGAATGTGGAAGAGTCTGAATTAACATATGTTGGCATGGTTCAACGTGATGTGTGCTCATTATCT
AATGGAATGTCCAAGTCAGTTGAGACAGCAATTTTGAATCCTCCTTTTGGGACCAAAAATAATAAAGGGACAGACATGGC
TTTTCCAAAGACCACTTTGGAAATGGCAAGAACAGCAGTATAT

Alignment

ORF - retro_ptro_1822 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.69 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HIAACMLYTIHNTYDDIENKVVADLGCGCGVLSIGTAMLGAGLCVGFDIDEDALEIFNRNAEEFELTNID
          H..A.MLYTIHNT.D..ENKV.ADLGCGCGVLS.GTAMLGA.L.VGFDID..AL.IFNRN.EE.ELT...
Retrocopy HSEAHMLYTIHNTCDEVENKVAADLGCGCGVLSLGTAMLGARLYVGFDIDAGALGIFNRNVEESELTYVG

Parental  MVQCDVCLLSNRMSKSFDTVIMNPPFGTKNNKGTDMAFLKTALEMARTAVY
          MVQ.DVC.LSN.MSKS..T.I.NPPFGTKNNKGTDMAF.KT.LEMARTAVY
Retrocopy MVQRDVCSLSNGMSKSVETAILNPPFGTKNNKGTDMAFPKTTLEMARTAVY

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	0.18 RPM	5.84 RPM
SRP007412_cerebellum	0.18 RPM	3.41 RPM
SRP007412_heart	0.03 RPM	11.16 RPM
SRP007412_kidney	0.10 RPM	9.68 RPM
SRP007412_liver	0.03 RPM	4.88 RPM
SRP007412_testis	0.32 RPM	10.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1822 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1822 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1822 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003343	1 retrocopy	retro_cpor_373,
Dasypus novemcinctus	ENSDNOG00000013460	2 retrocopies	retro_dnov_1043, retro_dnov_773,
Homo sapiens	ENSG00000138382	2 retrocopies	retro_hsap_1365, retro_hsap_2930,
Gorilla gorilla	ENSGGOG00000022484	2 retrocopies	retro_ggor_1064, retro_ggor_2032,
Loxodonta africana	ENSLAFG00000018044	2 retrocopies	retro_lafr_1213, retro_lafr_864,
Macaca mulatta	ENSMMUG00000023054	3 retrocopies	retro_mmul_1430, retro_mmul_1953, retro_mmul_2193,
Nomascus leucogenys	ENSNLEG00000005018	4 retrocopies	retro_nleu_1070, retro_nleu_1919, retro_nleu_753, retro_nleu_990,
Oryctolagus cuniculus	ENSOCUG00000010405	1 retrocopy	retro_ocun_1440,
Pongo abelii	ENSPPYG00000012916	2 retrocopies	retro_pabe_2281, retro_pabe_2523,
Pan troglodytes	ENSPTRG00000012621	3 retrocopies	retro_ptro_1822 , retro_ptro_2062, retro_ptro_938,