RetrogeneDB ID: retro_ptro_2062

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:74796639..74797269(-)
• 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_2062
GTGAAGAAATTAAGGCTTAAAGGCCTACAATGTCAGCTGCATTAAGTGGATGGATTCAAACAGCCAGGTGACTTCTAGAA
TAGTACCTGGCCAGCGTGTATATTTAAGCCTGTGTGCTCTATACAATCCACTACACAGGGGATGACATTGAAATTAAAGT
GGTTGCAGATCTAGAACATGGTGGTAGAGTGCTTAGCATCCAAGCTACAATGGTAGGAGCAGGGTTGTGGTTGTATTGGA
CATAGATGAAGATGCATTGAAAATATTTAATAGGAATGTGGAAGAGTTTGACTTAGCAAATGTTGTCATGGTTTACTGTG
ATATGTGCTCATAATTTAAGAGAATGTCCAAGTCATTAGATACAGTAATCATGAATCCTCACTTTGGGACCAAAAATAAT
AAAGTTATATTCAAAGATATAACTTCTCTGAAGACTGCTTCAGAAATGGCAAGGACAGTCATATATATTTTGCACAAATC
CTCAACTACAAAACATGCTCAAAAGAAAGTTGCAGAATAGAAAATCGAGATAAATGTTATTACAGAGTTGAGATACGACC
TGCCAGCATCATGCAATTGTCATAAAAAGAGATCAGTGGATGTTGAAGTGAACTAATTCAGTTTTCTTTT

Alignment

ORF - retro_ptro_2062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKKVRLKELESRLQQVDGFEKP-KLLLEQYPTRPHIAACMLYTIHNTYDDIENKVVADLGCGCGVLSIGT
          .KK.RLK.L...L..VDGF..P...LLE.Y.....I.AC.LYTIH.T.DDIE.KVVADL..G..VLSI..
Retrocopy VKKLRLKGLQCQLH*VDGFKQP<R*LLE*YLASVYI*ACVLYTIHYTGDDIEIKVVADLEHGGRVLSIQA

Parental  AMLGAGL-CVGFDIDEDALEIFNRNAEEFELTNIDMVQCDVCLLSNRMSKSFDTVIMNPPFGTKNNKGT-
          .M.GAGL..V..DIDEDAL.IFNRN.EEF.L.N..MV.CD.C....RMSKS.DTVIMNP.FGTKNNK...
Retrocopy TMVGAGL<VVVLDIDEDALKIFNRNVEEFDLANVVMVYCDMCS*FKRMSKSLDTVIMNPHFGTKNNKVIF

Parental  -DMAFLKTALEMARTAVYSLHKSSTREHVQKKAAEWKIKIDIIAELRYDLPASYKFHKKKSVDIEV-DLI
          .D...LKTA.EMART..Y.LHKSST..H.QKK.AE.KI.I..I.ELRYDLPAS...HKK.SVD.EV..LI
Retrocopy KDITSLKTASEMARTVIYILHKSSTTKHAQKKVAE*KIEINVITELRYDLPASCNCHKKRSVDVEV<ELI

Parental  RFSF
          .FSF
Retrocopy QFSF

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	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	0.00 RPM	10.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2062 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2062 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2062 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2930
Gorilla gorilla	retro_ggor_2032
Pongo abelii	retro_pabe_2523
Macaca mulatta	retro_mmul_1953
Callithrix jacchus	retro_cjac_2282

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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,