RetrogeneDB ID: retro_pvam_150

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_164:312679..313181(-)
• Located in intron of: ENSPVAG00000016472

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL47
• Ensembl ID: ENSPVAG00000004284
• Aliases: None
• Description: mitochondrial ribosomal protein L47 [Source:HGNC Symbol;Acc:16652]

Sequence

>retro_pvam_150
GGGTGGCGGGTGGTAAAAACTGGAGCTTCCTGGAACTGTGAGCAATTAAGAACGAAAATAATTAAGATATACATAAATTT
TAGTATGTCCTATTAAAAAAAGAAACATGCTCCTAACTCTGGAGTAGAAGGCCAAGTGGCAGAGATCGCTAATGCCAAGT
CTGGAATGATTAGAAAAGTAGTAGATCCCATGGATACATTTGATAAAGTTGTCCAGGAAGATGCCTTAAGGTTTTTCCAG
ACTGCGCCAGCTAGACCTGGTGCTGTGATAAGAGACATCTTTGGAAGAACCATCTCACACAGTTCAAGAAGTGGCCTGTA
TCTTGGTACCTAAGTAACAGATACAACAGGAAATGATTCTTTGCAATGTCCTATGTGAAACAGTTTGTTAGACTGAGACT
TGAGAACAAGCCCACATTGAAGCAAGAAAGAAAAGTATAGAGAAAAAAAAATTTCTTCAGGAAAAGTTTCCACATCTTTC
TAAAGTCCAGAAGTCAAGACTT

Alignment

ORF - retro_pvam_150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.56 %
• Parental protein coverage: 70.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GEEKVKSGASWTCQQLR-NKSNEDLHKLWYVLLKE-RNMLLTLEQEAKRQVLPMPSPERLE-KVIESMDA
          G...VK.GASW.C.QLR.N..N.D.HK..YVLLK..RNMLLTLE..AK.Q...MPS.E.LE.KV...MD.
Retrocopy GWRVVKTGASWNCEQLR<NENN*DIHKF*YVLLKK<RNMLLTLE*KAKWQRSLMPSLE*LE<KVVDPMDT

Parental  LDKVVQEREDALRLLQTGQEKARPGAWRRDIFGRVFWH-KFKQWPIPWYLNKKYNRKRFFAMPYVEHFDR
          .DKVVQ..EDALR..QT....ARPGA..RDIFGR...H..FK.WP..WYL...YNRK.FFAM.YV..F.R
Retrocopy FDKVVQ--EDALRFFQTA--PARPGAVIRDIFGRTISH<QFKKWPVSWYLSNRYNRK*FFAMSYVKQFVR

Parental  LRRE-KQARIEARKKTLQKKKARLLQEKFPHLSEAQKSSL
          LR.E..QA.IEARKK.........LQEKFPHLS..QKS.L
Retrocopy LRLE<EQAHIEARKKSIE--XXXFLQEKFPHLSKVQKSRL

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_150 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011380	1 retrocopy	retro_cfam_1085,
Cavia porcellus	ENSCPOG00000002312	2 retrocopies	retro_cpor_1219, retro_cpor_885,
Felis catus	ENSFCAG00000031548	1 retrocopy	retro_fcat_235,
Macropus eugenii	ENSMEUG00000012649	2 retrocopies	retro_meug_1039, retro_meug_146,
Monodelphis domestica	ENSMODG00000021301	3 retrocopies	retro_mdom_1361, retro_mdom_1879, retro_mdom_562,
Mustela putorius furo	ENSMPUG00000017214	1 retrocopy	retro_mputfur_495,
Mus musculus	ENSMUSG00000037531	3 retrocopies	retro_mmus_1976, retro_mmus_1986, retro_mmus_2753,
Otolemur garnettii	ENSOGAG00000016957	2 retrocopies	retro_ogar_1900, retro_ogar_3015,
Pteropus vampyrus	ENSPVAG00000004284	1 retrocopy	retro_pvam_150 ,
Rattus norvegicus	ENSRNOG00000011639	2 retrocopies	retro_rnor_1829, retro_rnor_2523,
Sorex araneus	ENSSARG00000006898	2 retrocopies	retro_sara_269, retro_sara_721,
Tursiops truncatus	ENSTTRG00000008909	1 retrocopy	retro_ttru_420,