RetrogeneDB ID: retro_ptro_938

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:74137026..74137591(+)
• Located in intron of: None

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_938
AAGGAATTAAGGCTTAAGGAACTAGAGAGTCACCTGCAATAAGTGGATGGATTCGAAAAGGCCAAGCTACTTCTAGAACA
GTATCCCACCAAGCTTCACATTGCAGCATGTATGCTGTATGCAATCCATAGCACTTATGATGACATTGAAAGTGAAGTTT
TTGCAGATCTAGGCTGTAGTGGTGGAATGCTTAGCATGGGAACTGCAGTGTGAGGAGCAGGGTTCTGTGTTGGATTTGAC
AGAGATGAAGATGTATTGGAAATAGTTAATAGGAATGTGGAAGAGTTTGAGTTAACAAATATTGACATGGTTCAATGTGA
TGTGTGCCTGTTATCTAACAGGATGTCAAGTCATTTGATACAGTAATTATGAATCCGCCTTTTGGGACCAAAAATAATAA
AGGGATAGATATGGCTTTTCTAAAGACCGCTTTGGAAATGGCAAGAACAGCAGTATATTCTTTACACAAATCCTCAGAGA
ACATGTTGAAAAGAAAGCTGCAGAATGGGAAATCAAGATAGATATGATTTCAGAGCTTCAGGATGACCTGCCAGCATCAT
ACAAG

Alignment

ORF - retro_ptro_938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.65 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKVRLKELESRLQQVDGFEKPKLLLEQYPTRPHIAACMLYTIHNTYDDIENKVVADLGCGCGVLSIGTAM
          K..RLKELES.LQ.VDGFEK.KLLLEQYPT..HIAACMLY.IH.TYDDIE..V.ADLGC..G.LS.GTA.
Retrocopy KELRLKELESHLQ*VDGFEKAKLLLEQYPTKLHIAACMLYAIHSTYDDIESEVFADLGCSGGMLSMGTAV

Parental  LGAGLCVGFDIDEDALEIFNRNAEEFELTNIDMVQCDVCLLSNRMS-KSFDTVIMNPPFGTKNNKGTDMA
          .GAG.CVGFD.DED.LEI.NRN.EEFELTNIDMVQCDVCLLSNRMS.KSFDTVIMNPPFGTKNNKG.DMA
Retrocopy *GAGFCVGFDRDEDVLEIVNRNVEEFELTNIDMVQCDVCLLSNRMS<KSFDTVIMNPPFGTKNNKGIDMA

Parental  FLKTALEMARTAVYSLHKSSTREHVQKKAAEWK-IKIDIIAELRYDLPASYK
          FLKTALEMARTAVYSLHKSS.......K....K.IKID.I.EL..DLPASYK
Retrocopy FLKTALEMARTAVYSLHKSS-ENMLKRKLQNGK<IKIDMISELQDDLPASYK

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	0.07 RPM	5.84 RPM
SRP007412_cerebellum	0.00 RPM	3.41 RPM
SRP007412_heart	0.00 RPM	11.16 RPM
SRP007412_kidney	0.00 RPM	9.68 RPM
SRP007412_liver	0.00 RPM	4.88 RPM
SRP007412_testis	0.11 RPM	10.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_938 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_938 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1365
Gorilla gorilla	retro_ggor_1064
Macaca mulatta	retro_mmul_2193
Callithrix jacchus	retro_cjac_729

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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 ,