RetrogeneDB ID: retro_pvam_167

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1726:176710..177097(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF4
• Ensembl ID: ENSPVAG00000017017
• Aliases: None
• Description: ring finger protein 4 [Source:HGNC Symbol;Acc:10067]

Sequence

>retro_pvam_167
GGCATAGATCACTTATTTCTCTGAAGACTGGATGCAAAAAGCACAATGAATACAAGTATGTGCTATGGTAGCATGGTGAA
TTCCAGACAAGCCCGAGAATGCCGTACAGCTGGGGAGGGAGGGCCAACTCCTGAGATGGTCTTGGAAGCAGAACTGATAG
AACTTGGGGAAAGTGATGAAGTTGTTGACCTAACATCTGAATCTCTAGAACCTGCAGTGATTGACCTTACTCACCATGAC
TCTGTTGTGATTACTGGAGAAAGGAGGAGGCCAAGGAGAAAAACAAGGTTACTCCAAGGCCAAACTGGCAGCAGTGTGGG
GAGCAGTGATAAGAATGGGTTGATGATGGACGGAGATGTATATGTGATCAGCAGTGCCTACCATAAT

Alignment

ORF - retro_pvam_167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 75.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPGHLLL--VAPRSTMSTRKRRGGTLSSRQAQK-RTR-EAASTPEMALEAEPIELVESAGDEIVDLTCES
          G..HL.L......STM.T....G....SRQA...RT..E...TPEM.LEAE.IEL.ES..DE.VDLT.ES
Retrocopy GIDHLFL*RLDAKSTMNTSMCYGSMVNSRQARECRTAGEGGPTPEMVLEAELIELGES--DEVVDLTSES

Parental  LEPVVVDLTHNDSVVV-GERRRPRRTARRLRQDHADSCVVSSDDEELARDRDVYVTTHTPRN
          LEP.V.DLTH.DSVV..GERRRPRR...RL.Q....S.V.SSD...L..D.DVYV......N
Retrocopy LEPAVIDLTHHDSVVITGERRRPRRKT-RLLQGQTGSSVGSSDKNGLMMDGDVYVISSAYHN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_167 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014366	1 retrocopy	retro_amel_77,
Canis familiaris	ENSCAFG00000014856	1 retrocopy	retro_cfam_25,
Equus caballus	ENSECAG00000024877	1 retrocopy	retro_ecab_33,
Homo sapiens	ENSG00000063978	1 retrocopy	retro_hsap_319,
Gorilla gorilla	ENSGGOG00000015149	2 retrocopies	retro_ggor_1144, retro_ggor_345,
Loxodonta africana	ENSLAFG00000007382	1 retrocopy	retro_lafr_44,
Microcebus murinus	ENSMICG00000001767	1 retrocopy	retro_mmur_1265,
Mus musculus	ENSMUSG00000029110	1 retrocopy	retro_mmus_522,
Nomascus leucogenys	ENSNLEG00000000160	2 retrocopies	retro_nleu_1713, retro_nleu_37,
Oryctolagus cuniculus	ENSOCUG00000004998	2 retrocopies	retro_ocun_1566, retro_ocun_162,
Otolemur garnettii	ENSOGAG00000010776	1 retrocopy	retro_ogar_2121,
Pongo abelii	ENSPPYG00000025865	2 retrocopies	retro_pabe_1240, retro_pabe_36,
Pteropus vampyrus	ENSPVAG00000017017	1 retrocopy	retro_pvam_167 ,
Ictidomys tridecemlineatus	ENSSTOG00000011101	2 retrocopies	retro_itri_1108, retro_itri_171,
Tarsius syrichta	ENSTSYG00000011244	1 retrocopy	retro_tsyr_1606,