RetrogeneDB ID: retro_pvam_534

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3647:64600..64946(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL51
• Ensembl ID: ENSPVAG00000012566
• Aliases: None
• Description: mitochondrial ribosomal protein L51 [Source:HGNC Symbol;Acc:14044]

Sequence

>retro_pvam_534
GGCAGGCAGCTATGCAGCTGGGTGCCCTGGATCTGCAGAAGCTTCTCTCTGGGTGTTCCTGGATTGTTAATGTAAGTCTC
ACCCTCCTGCTCCCAAAATGATTGATCGCTGAAACTAGAAAAGGGCCTTGTTCTGGGTGTATAATTATGTCAGAATCCTG
AGGAGTTTTTTAAAGCACCACAAAGAATTAATCAAGGGCCTCAGATGGCTTTGAGGCTGGAAGATGAACGAATTGCGGTG
TTGTATCTGAAAGAAAATGGTTGGAATTCAGATGTTCCCTGAGGACCTGCCCAACCTTAACAAATGCATCAGCTATCTCT
ACAAACACTTTAACAGACTTGGAAAG

Alignment

ORF - retro_pvam_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.23 %
• Parental protein coverage: 91.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GRRLWGWVLPACRSFSLGVPGLL-HVRLTL-PPPKVVDRWNEKRAMFGVYDNIGILGNFEKHPKELIKGP
          GR.L..WV...CRSFSLGVPGLL..V.LTL.P.PK..DR.N.KRA.F.VY....IL..F.KH.KELIKG.
Retrocopy GRQLCSWVPWICRSFSLGVPGLL<NVSLTL<PAPKMIDR*N*KRALFWVYNYVRILRSFLKHHKELIKGL

Parental  RWLRGWKGNELQRCIRKKKMVGNRMFFDDLHNLNKRISYLYKHFNRHGK
          RWL.GWK.NEL..CI..KKMVG..MF..DL.NLNK.ISYLYKHFNR.GK
Retrocopy RWL*GWKMNELRCCI-*KKMVGIQMFPEDLPNLNKCISYLYKHFNRLGK

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_534 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014729	1 retrocopy	retro_btau_1609,
Callithrix jacchus	ENSCJAG00000018232	1 retrocopy	retro_cjac_548,
Cavia porcellus	ENSCPOG00000008478	1 retrocopy	retro_cpor_1082,
Loxodonta africana	ENSLAFG00000002106	2 retrocopies	retro_lafr_1157, retro_lafr_845,
Mus musculus	ENSMUSG00000030335	2 retrocopies	retro_mmus_1967, retro_mmus_2607,
Pteropus vampyrus	ENSPVAG00000012566	1 retrocopy	retro_pvam_534 ,
Rattus norvegicus	ENSRNOG00000019165	2 retrocopies	retro_rnor_2582, retro_rnor_926,
Tupaia belangeri	ENSTBEG00000000936	2 retrocopies	retro_tbel_3219, retro_tbel_3408,