RetrogeneDB ID: retro_pvam_449

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3196:30369..30678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED21
• Ensembl ID: ENSPVAG00000013357
• Aliases: None
• Description: mediator complex subunit 21 [Source:HGNC Symbol;Acc:11473]

Sequence

>retro_pvam_449
ATGGTAGATTGGCTCACACAGCTGCACGTGAACTTACTTGTAGATAAGTTTTGTAATGCCATTGGAGTGTTGCAGCAGAG
TGATGATCCTCCTGCCTCTTTTAGTAATATGTAGACAGCAATTAACAAAGATCAGCAGGCTAATTCTACAGAAGAATTCT
ACAGGCTTTTTGCAGCACTGATTGCATGAACAGTAAGAGACATCAACGTTTTGATAGGTATCTTGCCCAGTGAAGAATCT
ATAGCTGCTTTACAGGCTGCTGGCTTGTAGAAGCTAAAAGAAGAAAACCATGAAGCTGCTACATGTCTG

Alignment

ORF - retro_pvam_449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.38 %
• Parental protein coverage: 72.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADRLTQLQDAVNSLADQFCNAIGVLQQCG-PPASFSNIQTSINKDQPANPTEEYAQLFAALIARTAKDI
          M.D.LTQL...VN.L.D.FCNAIGVLQQ...PPASFSN..T.INKDQ.AN.TEE...LFAALIA.T..DI
Retrocopy MVDWLTQLH--VNLLVDKFCNAIGVLQQSDDPPASFSNM*TAINKDQQANSTEEFYRLFAALIA*TVRDI

Parental  DVLIDSLPSEESTAALQAASLYKLEEENHEAATCL
          .VLI..LPSEES.AALQAA.L.KL.EENHEAATCL
Retrocopy NVLIGILPSEESIAALQAAGL*KLKEENHEAATCL

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_449 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011670	1 retrocopy	retro_amel_108,
Dasypus novemcinctus	ENSDNOG00000010041	1 retrocopy	retro_dnov_998,
Homo sapiens	ENSG00000152944	1 retrocopy	retro_hsap_4105,
Gorilla gorilla	ENSGGOG00000016313	1 retrocopy	retro_ggor_2756,
Myotis lucifugus	ENSMLUG00000007678	1 retrocopy	retro_mluc_229,
Macaca mulatta	ENSMMUG00000003218	1 retrocopy	retro_mmul_2365,
Pongo abelii	ENSPPYG00000004377	1 retrocopy	retro_pabe_3361,
Pan troglodytes	ENSPTRG00000004785	1 retrocopy	retro_ptro_2786,
Pteropus vampyrus	ENSPVAG00000013357	1 retrocopy	retro_pvam_449 ,
Ictidomys tridecemlineatus	ENSSTOG00000008391	2 retrocopies	retro_itri_1005, retro_itri_1057,