RetrogeneDB ID: retro_pvam_477

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3369:14565..14912(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT4H1
• Ensembl ID: ENSPVAG00000002320
• Aliases: None
• Description: suppressor of Ty 4 homolog 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:11467]

Sequence

>retro_pvam_477
ATGGCTTTGGAGATGGTGCCAAATGACCTGTGGCATCTGCGGGCTTGTTTGCTATGTTTGCTGGTTGAGACTATAGACCA
GTTTGAATATGACAGTTGTAACAATTGTGATGCATACCTTCAAAAGAAGAGTAACCAAGAGATGATATATGACTGCACCA
TCTCTTCCTTTGATGGAATTATTGCAATGATGAGTCCAGAGGACAGCTGGGTTTCTAAGTGGCAGTGAGTCAGTAACTTT
AAGCCCAGTGTGTACACAGTATCAGTCACTAGTTGCCTTCCCCAGGGATCAAGCGGGAGCTGAGAAGTCAAGTGGCCTAC
AAATCCAGAGACACAGCTATAAAGACC

Alignment

ORF - retro_pvam_477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSW
          MALE.VP.DL.HLRACLLC.LV.TIDQFEYD.C.NCDAYLQ.K.N.EM.YDCT.SSFDGIIAMMSPEDSW
Retrocopy MALEMVPNDLWHLRACLLCLLVETIDQFEYDSCNNCDAYLQKKSNQEMIYDCTISSFDGIIAMMSPEDSW

Parental  VSKWQRVSNFKPGVYAVSVTGRLPQ-GIVRELKSRGVAYKSRDTAIKT
          VSKWQ.VSNFKP.VY.VSVT..LPQ.GI.REL.S..VAYKSRDTAIKT
Retrocopy VSKWQ*VSNFKPSVYTVSVTSCLPQ<GIKRELRSQ-VAYKSRDTAIKT

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_477 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017524	2 retrocopies	retro_cfam_1399, retro_cfam_553,
Homo sapiens	ENSG00000213246	2 retrocopies	retro_hsap_1081, retro_hsap_2280,
Gorilla gorilla	ENSGGOG00000007232	2 retrocopies	retro_ggor_1693, retro_ggor_854,
Macropus eugenii	ENSMEUG00000010164	1 retrocopy	retro_meug_2079,
Myotis lucifugus	ENSMLUG00000025583	1 retrocopy	retro_mluc_761,
Macaca mulatta	ENSMMUG00000007579	2 retrocopies	retro_mmul_1005, retro_mmul_842,
Mus musculus	ENSMUSG00000020485	2 retrocopies	retro_mmus_2857, retro_mmus_633,
Nomascus leucogenys	ENSNLEG00000008159	3 retrocopies	retro_nleu_1619, retro_nleu_1962, retro_nleu_2714,
Oryctolagus cuniculus	ENSOCUG00000025823	2 retrocopies	retro_ocun_1613, retro_ocun_1636,
Pongo abelii	ENSPPYG00000008233	1 retrocopy	retro_pabe_1940,
Pan troglodytes	ENSPTRG00000009451	2 retrocopies	retro_ptro_1614, retro_ptro_735,
Pteropus vampyrus	ENSPVAG00000002320	1 retrocopy	retro_pvam_477 ,
Rattus norvegicus	ENSRNOG00000007845	3 retrocopies	retro_rnor_1255, retro_rnor_1973, retro_rnor_556,