RetrogeneDB ID: retro_pabe_2523

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:64891562..64892192(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL5
• Ensembl ID: ENSPPYG00000012916
• Aliases: None
• Description: methyltransferase like 5 [Source:HGNC Symbol;Acc:25006]

Sequence

>retro_pabe_2523
GTGAAGAAATTAAGGCTTAAAGGCCTACAGTGTCAGCTGTAATAAGTGGATGGATTCAAATAGCCAGGCTACTTCTAGAA
TAGTACCCGGCCAGCGTGTATGTTTAAGCCTGTGTGCTCTATGCAATCCACTACACATGGAATGACATTGAAATTGAAGT
GGTTGCAGATCTAGAATATGGTGGTAGAGTGCTTAGCATCCAAGCTACAATGGTAGGAGCAGGGTTGTGGTTGTATTGGA
CATAGATGAAGATGCACTGAAAATATTTATTAGGAATGTGGAAGAGTTTGACTTAGCAAATGTTGTCATGGTTTACTGTG
ATATGTGCTCATAATTTAAGAGAATGTCCAAGTCATTAGATACAGTAATCATGAATCCTCACTTTGGGACCAAAAATAAT
AAAGTTATATTCAAAGATATAACTTCTCTGAAGACTGCTTCGGAAATGACAAGGACAGTCGTATATATTTTGCACAAATC
CTCAACTACAAAACATGCTCAAAAGAAAGTTGCAGAATAGAAAATGGAGATAGATGTTATTACAGAGTTGAGATCCGACC
TGCCAGCATCATGCAACTGTCATAAAAAGAGATCGGTGGATGTTGAAGCGAACTAATTCAGTTTTCTTTT

Alignment

ORF - retro_pabe_2523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKKVRLKELESRLQQVDGFEKP-KLLLEQYPTRPHIAACMLYTIHNTYDDIENKVVADLGCGCGVLSIGT
          .KK.RLK.L...L..VDGF..P..LLLE.YP......AC.LY.IH.T..DIE..VVADL..G..VLSI..
Retrocopy VKKLRLKGLQCQL**VDGFK*P<RLLLE*YPASVYV*ACVLYAIHYTWNDIEIEVVADLEYGGRVLSIQA

Parental  AMLGAGL-CVGFDIDEDALEIFNRNAEEFGLTNIDMVQCDVCLLSNRMSKSFDTVIMNPPFGTKNNKGT-
          .M.GAGL..V..DIDEDAL.IF.RN.EEF.L.N..MV.CD.C....RMSKS.DTVIMNP.FGTKNNK...
Retrocopy TMVGAGL<VVVLDIDEDALKIFIRNVEEFDLANVVMVYCDMCS*FKRMSKSLDTVIMNPHFGTKNNKVIF

Parental  -DMAFLKTALEMARTAVYSLHKSSTREHVQKKAAEWKIKIDIIAELRYDLPASYKFHKKKSVDIEV-DLI
          .D...LKTA.EM.RT.VY.LHKSST..H.QKK.AE.K..ID.I.ELR.DLPAS...HKK.SVD.E...LI
Retrocopy KDITSLKTASEMTRTVVYILHKSSTTKHAQKKVAE*KMEIDVITELRSDLPASCNCHKKRSVDVEA<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	5.42 RPM
SRP007412_cerebellum	0.00 RPM	2.80 RPM
SRP007412_heart	0.00 RPM	13.03 RPM
SRP007412_kidney	0.00 RPM	5.40 RPM
SRP007412_liver	0.00 RPM	2.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2523 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2523 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2523 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2930
Pan troglodytes	retro_ptro_2062
Gorilla gorilla	retro_ggor_2032
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,