RetrogeneDB ID: retro_pvam_1400

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_79:184025..184380(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNPH1
• Ensembl ID: ENSPVAG00000008743
• Aliases: None
• Description: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [Source:HGNC Symbol;Acc:21218]

Sequence

>retro_pvam_1400
TACATATATTCTATAGAATACAGTTCATCTAGAGAAGAGGCTGCTTGGGTCAACAAGCTCATCCATGAGTGGGAACTGCC
TTCATTGCAATAGGCAGAAATGGTCATGGCAGAAGTGACCCAGCCATCCTTATGTGTAGGCTATGAGGTGGGCCAGGCTA
TGGCTCCCAGTAAGTGAATCCTGTGCCTGCTCTTCCTACAGTCTGGCTGAGTGTTTTCAGACTTGATCACAGGAGCAACA
TGTGGCTGGTGGTTCCAGGTGTGGACTACAAAGAGTGGGAGGGGAGGCCATAATGGATCAACATTTTGGGGCTGAAGCTC
CCGACCAGATGGCTGCCTTCTCTGACCCAACCACT

Alignment

ORF - retro_pvam_1400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.24 %
• Parental protein coverage: 68.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HVAAAELSARGEEAARGDRLIHDQDLAWLQQADVVVAEVTQPSLGVGYELGRAVALNKRILCLFRPQSGR
          .....E.S...EEAA....LIH...L..LQ.A..V.AEVTQPSL.VGYE.G.A.A..K.ILCL...QSG.
Retrocopy YIYSIEYSSSREEAAWVNKLIHEWELPSLQ*AEMVMAEVTQPSLCVGYEVGQAMAPSK*ILCLLFLQSG*

Parental  VLSAMIRGAADGSRFQVW-DYEERE-VEAMLDRYFEADPPEQVASSPAPTT
          V.S..I.GA..G..FQVW.DY.E.E..EA..D..F.A..P.Q.A....PTT
Retrocopy VFSDLITGATCGWWFQVW<DYKEWE<GEAIMDQHFGAEAPDQMAAFSDPTT

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_1400 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012390	1 retrocopy	retro_amel_1012,
Bos taurus	ENSBTAG00000019913	1 retrocopy	retro_btau_518,
Canis familiaris	ENSCAFG00000001837	1 retrocopy	retro_cfam_1148,
Callithrix jacchus	ENSCJAG00000005337	1 retrocopy	retro_cjac_3948,
Equus caballus	ENSECAG00000006660	1 retrocopy	retro_ecab_595,
Felis catus	ENSFCAG00000009722	1 retrocopy	retro_fcat_365,
Homo sapiens	ENSG00000112667	1 retrocopy	retro_hsap_2562,
Nomascus leucogenys	ENSNLEG00000000516	1 retrocopy	retro_nleu_1515,
Pongo abelii	ENSPPYG00000016635	1 retrocopy	retro_pabe_1888,
Pan troglodytes	ENSPTRG00000029662	1 retrocopy	retro_ptro_1493,
Pteropus vampyrus	ENSPVAG00000008743	1 retrocopy	retro_pvam_1400 ,
Rattus norvegicus	ENSRNOG00000018397	1 retrocopy	retro_rnor_580,
Tursiops truncatus	ENSTTRG00000007022	1 retrocopy	retro_ttru_1520,