RetrogeneDB ID: retro_pvam_450

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3199:12522..12912(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSPVAG00000005511
• Aliases: None
• Description: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Source:HGNC Symbol;Acc:11158]

Sequence

>retro_pvam_450
GCCATCCAAACTCCAGTCTGTAGGCCCTTGGTTGTCGGGTGTTGTGCACTCTCGGACAGAAAGAGTGATGGTGCTGCTAG
GATGAAGGTCGTGAGATTTTTGATGAAATTGAGTCACGAAACTGTAACAACCGAATTAAAGAATGGGATACAGGTCCATG
GAACAATCGCAGGTGTAGATGTCAGCATGAATACGCACCATAAAGCTGTGAAAATGACCCTGAAGAACTGAGAACCTGTA
TAACTGGAAACACTGAGTATTTGAGGAAATAACATTCGATTTTGTATTCTGCCAGACAGCTTACTTCTGGATATGCTACT
CATGGATGTTGAACCAAAAATGAGATCTAAGAGAAGGGAAGCTGTTGTAGGCCAGGGCAGAAGAAGAGGG

Alignment

ORF - retro_pvam_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.54 %
• Parental protein coverage: 87.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AIHTPVRRPLVVGFCAFSDRRSDGAARMKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAV
          AI.TPV.RPLVVG.CA.SDR.SDGAARMK.VRFLMKLSHETVT.ELKNG.QVHGTI.GVDVSMNTH.KAV
Retrocopy AIQTPVCRPLVVGCCALSDRKSDGAARMKVVRFLMKLSHETVTTELKNGIQVHGTIAGVDVSMNTHHKAV

Parental  KMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRG
          KMTLKN.EPV.LETLSI.GNNIR..ILPDSL.LD.LL.DVEPK..SK.REAV.G.GR.RG
Retrocopy KMTLKN*EPV*LETLSI*GNNIRFCILPDSLLLDMLLMDVEPKMRSKRREAVVGQGRRRG

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_450 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Canis familiaris	ENSCAFG00000018247	1 retrocopy	retro_cfam_373,
Dasypus novemcinctus	ENSDNOG00000018773	4 retrocopies	retro_dnov_1254, retro_dnov_1716, retro_dnov_1832, retro_dnov_2403,
Felis catus	ENSFCAG00000012352	1 retrocopy	retro_fcat_1885,
Macaca mulatta	ENSMMUG00000003992	2 retrocopies	retro_mmul_887, retro_mmul_891,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Pongo abelii	ENSPPYG00000025874	3 retrocopies	retro_pabe_254, retro_pabe_948, retro_pabe_952,
Pan troglodytes	ENSPTRG00000009909	2 retrocopies	retro_ptro_291, retro_ptro_781,
Pteropus vampyrus	ENSPVAG00000005511	1 retrocopy	retro_pvam_450 ,
Rattus norvegicus	ENSRNOG00000013714	2 retrocopies	retro_rnor_2671, retro_rnor_2729,
Tursiops truncatus	ENSTTRG00000002654	2 retrocopies	retro_ttru_1566, retro_ttru_1890,