RetrogeneDB ID: retro_pvam_305

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2428:86562..87009(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000003763
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NCBP2
• Ensembl ID: ENSPVAG00000017273
• Aliases: None
• Description: nuclear cap binding protein subunit 2, 20kDa [Source:HGNC Symbol;Acc:7659]

Sequence

>retro_pvam_305
CTGAAGATTTTGTGCAGTGACTCCTACCTGAAGCTGAGCAATTACCGGGACCAGCAGTTCAGTGGCGATAACCAAGAGCA
TGAAAAATTACTGAAGGAAAGCTGCACGCTGTATGTGGGGAATCTTTCCTTTTATATAACTGAAGAGCAGATATTTGAGC
TCTTTACTAGATGTGGTGATCTCAGGAATGTATTTATGGGCTTGGATAAAATAAAGAAAATGACATGTGGTTTCTGTTTT
ATAGAATACTATAGCAGAGCTGATGCGGAAAATGCCATGCGGTTCCTAAATGGGACCTTCTTAGATGACCGTATCATCCG
CACAGACTGGGATCTAGGCTTTTGAGAGGGCAGACAGTATGGCCATGGCTGGTCCGGGGGCCTGGTAAGAGATGAGTTTC
GTGAAGACTTTGATGCTGGTAGAGGAAGCTTTGGAAAACAAGCTCAG

Alignment

ORF - retro_pvam_305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.83 %
• Parental protein coverage: 95.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK
          LK.L.SDSY..LS.YRDQ.F.GDN.E.EKLLK.SCTLYVGNLSFY.TEEQI.ELF...GD.....MGLDK
Retrocopy LKILCSDSYLKLSNYRDQQFSGDNQEHEKLLKESCTLYVGNLSFYITEEQIFELFTRCGDLRNVFMGLDK

Parental  MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRLIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAG
          .KK..CGFCF.EYYSRADAENAMR..NGT.LDDR.IRTDWD.GF.EGRQYG.G.SGG.VRDE.R.D.DAG
Retrocopy IKKMTCGFCFIEYYSRADAENAMRFLNGTFLDDRIIRTDWDLGF*EGRQYGHGWSGGLVRDEFREDFDAG

Parental  RGGYGKLAQ
          RG..GK.AQ
Retrocopy RGSFGKQAQ

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_305 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 25 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003664	2 retrocopies	retro_amel_113, retro_amel_62,
Bos taurus	ENSBTAG00000008873	1 retrocopy	retro_btau_1819,
Canis familiaris	ENSCAFG00000013100	2 retrocopies	retro_cfam_152, retro_cfam_2195,
Callithrix jacchus	ENSCJAG00000013735	2 retrocopies	retro_cjac_3139, retro_cjac_4103,
Cavia porcellus	ENSCPOG00000002976	1 retrocopy	retro_cpor_611,
Equus caballus	ENSECAG00000016153	1 retrocopy	retro_ecab_79,
Felis catus	ENSFCAG00000029865	2 retrocopies	retro_fcat_1936, retro_fcat_561,
Homo sapiens	ENSG00000114503	1 retrocopy	retro_hsap_5,
Loxodonta africana	ENSLAFG00000006372	1 retrocopy	retro_lafr_129,
Macropus eugenii	ENSMEUG00000004730	1 retrocopy	retro_meug_34,
Microcebus murinus	ENSMICG00000003162	1 retrocopy	retro_mmur_488,
Myotis lucifugus	ENSMLUG00000017500	2 retrocopies	retro_mluc_355, retro_mluc_592,
Mustela putorius furo	ENSMPUG00000003806	1 retrocopy	retro_mputfur_9,
Mus musculus	ENSMUSG00000022774	2 retrocopies	retro_mmus_2381, retro_mmus_2645,
Nomascus leucogenys	ENSNLEG00000001727	1 retrocopy	retro_nleu_1239,
Oryctolagus cuniculus	ENSOCUG00000006738	2 retrocopies	retro_ocun_1887, retro_ocun_833,
Otolemur garnettii	ENSOGAG00000005009	6 retrocopies	retro_ogar_3151, retro_ogar_3152, retro_ogar_3153, retro_ogar_3160, retro_ogar_3161, retro_ogar_3162,
Pongo abelii	ENSPPYG00000014449	1 retrocopy	retro_pabe_85,
Pan troglodytes	ENSPTRG00000015789	1 retrocopy	retro_ptro_3151,
Pteropus vampyrus	ENSPVAG00000017273	3 retrocopies	retro_pvam_238, retro_pvam_305 , retro_pvam_939,
Sarcophilus harrisii	ENSSHAG00000004363	2 retrocopies	retro_shar_161, retro_shar_46,
Tupaia belangeri	ENSTBEG00000015222	3 retrocopies	retro_tbel_2153, retro_tbel_3367, retro_tbel_758,
Tarsius syrichta	ENSTSYG00000014263	1 retrocopy	retro_tsyr_2008,
Tursiops truncatus	ENSTTRG00000013908	2 retrocopies	retro_ttru_442, retro_ttru_826,
Vicugna pacos	ENSVPAG00000010369	1 retrocopy	retro_vpac_493,