RetrogeneDB ID: retro_pvam_334

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2613:4020..4840(+)
• Located in intron of: ENSPVAG00000006438

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCTN4
• Ensembl ID: ENSPVAG00000014234
• Aliases: None
• Description: dynactin 4 (p62) [Source:HGNC Symbol;Acc:15518]

Sequence

>retro_pvam_334
CACACCCTCTCCACTCGGGCAACGAGCATCTCCATGCAGCTTCCAGATGACCCAGCCAAGTCCACCATGAAGAAGGTCTA
TTACCTGGCTTGTGGATTTTGTTGCTGGACATCTAGAGATGTGGGCATGGCAGACAAATCTGTGGCCAGTGGTGGTTGGC
AGGAACCTGAAAATCCTCACACACAGCGGATGAACAAACTGATTGAATATTACCAGCAGCTTGCTTAGAAAGAGAAGGTT
GAGCGAGATCGCAAGAAACTGGCACGGTGCAGAAACTATATGCCTTTGGCTTTTTCAGACAAATATGGTCATGGAACCAG
GCTTCAGCGACCATGAGCTAGTGCAACCATCAGTACCCTTGCCGGAGTTTTCCTTAAAGAAGGAGAGGACCAGAAAGATA
AAGATTGAGCCAGCTCAGGCTGTAGATGAAGTGGAGCCTCTACTCGAAGACTATTATAGAAGACCAGTAAATTTAACAGA
GATGATCACCCTTCAGCAGTGCCTCTTACAGCCTGACTTCCAACCAATCTGTGCATCCCAGCTCTATCCTCGTCACAAAC
ATCTTCTGATCAAATGGTCCCTGCCCTGCCAGAAATGTGAACATAATGTGAGCAAGCCAGAGTTTAATCTAACATCTATC
AAATTCAAAATCCAACTGGTTGCTGTCAATTATATTCCAGAAGTGAGGATCATATTAATTCCCAACCTTCGCTACATGAA
AGAGAGCCAGGTCCACCTGACTCTTATGAACTCAGTGGAGAACCTCACCCATGTGACCTTGTTGGAGTGTGATGAGGGAG
ACCCTCATCACAGGGGGTCT

Alignment

ORF - retro_pvam_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 59.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HTLSTRATSISTQLPDDPAKTTMKKAYYLACGFCRWTSRDVGMADKSVASGGWQEPENPHTQRMNKLIEY
          HTLSTRATSIS.QLPDDPAK.TMKK.YYLACGFC.WTSRDVGMADKSVASGGWQEPENPHTQRMNKLIEY
Retrocopy HTLSTRATSISMQLPDDPAKSTMKKVYYLACGFCCWTSRDVGMADKSVASGGWQEPENPHTQRMNKLIEY

Parental  YQQLAQKEKVERDRKKLARRRNYMPLAFSDKYGLGTRLQRPRAGATISTLAGL-SLKDGEDQKEIKIEPA
          YQQLA.KEKVERDRKKLAR.RNYMPLAFSDKYG.GTRLQRP.A.ATISTLAG..SLK..E....IKIEPA
Retrocopy YQQLA*KEKVERDRKKLARCRNYMPLAFSDKYGHGTRLQRP*ASATISTLAGV>SLKK-ERTRKIKIEPA

Parental  QAVDEVEPLPEDYYT-PVNLTEVTTLQQRLLQPDFQPICASQLYPRHKHLLIKRSLRCRKCEHNLSKPEF
          QAVDEVEPL.EDYY..PVNLTE..TLQQ.LLQPDFQPICASQLYPRHKHLLIK.SL.C.KCEHN.SKPEF
Retrocopy QAVDEVEPLLEDYYRRPVNLTEMITLQQCLLQPDFQPICASQLYPRHKHLLIKWSLPCQKCEHNVSKPEF

Parental  NPTSIKFKIQLVAVNYIPEVRIMSIPNLRYMKESQVLLTLTNPVENLTHVTLLECDEGDPDNINS
          N.TSIKFKIQLVAVNYIPEVRI..IPNLRYMKESQV.LTL.N.VENLTHVTLLECDEGDP....S
Retrocopy NLTSIKFKIQLVAVNYIPEVRIILIPNLRYMKESQVHLTLMNSVENLTHVTLLECDEGDPHHRGS

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_334 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000014234	1 retrocopy	retro_pvam_334 ,
Rattus norvegicus	ENSRNOG00000019298	1 retrocopy	retro_rnor_1305,
Ictidomys tridecemlineatus	ENSSTOG00000013446	1 retrocopy	retro_itri_830,