RetrogeneDB ID: retro_pvam_158

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1680:359736..360589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR45B
• Ensembl ID: ENSPVAG00000006212
• Aliases: None
• Description: WD repeat domain 45B [Source:HGNC Symbol;Acc:25072]

Sequence

>retro_pvam_158
CTCCAAATGGCATTTTGCTGCAACTGTTTTGCTTTAGTTGTTGGTGGAAAAGAAGCTGAAATACTTTCCCAATGAAACGT
TAATCTCGAATGATCTGAAAAAGAAGGTTGTTATTAAAACAGAGTTATCTACAGAAGTCGAGGTGGTCAAATTGAGGTGA
GATAGAATTATGGTCATTTTGGACCCCAAGACTAAAATGTTCACATGCACATACAGTTCCCATAATTTGCATGTCTTGGA
AACCTGCTATAACCCTAACGGACTTTATGTCTTGTGTCACAACAGCAGCAATTCCTTCCTGGCCCTCCCAGGCACGCACG
TGTGTCATGTGCAGCTTGTGGACCTGGCCAGCACCAAGTTACTGCCCATGGACATTCCCACACCCAAGGACATCCCGAGC
TGCATTGCTCTCAGCCTGTACAGGACAGAATTGCCATCCGTTAAAGGGACTCTTACAAGAATAATTTGCTACTTCATCAG
GGCGTCTAATCCAGGAACTATGAAGATGTGAAGCAGCAAATATTTATTGCATTAACCAGTCAAGATGCTTCCTGATCTGT
ATATCTTGTGATCATAGCACAGTGCACATTTCTGCTGTCAAAGATCCAAAAAAGGAACGAACAGTATAGTTTCACATCAG
CCAATTTCCTTGTGAAATACTTCAGTTCCAAATGAAGTTTGCCCAAATTTCAGGTTCCCTCAGGCTCTCCATGCATTCGC
ACTTTTGGAACAGTGTCAAATACTGTTATTTCACTTTGTGCAGCAGCAGCTACTATACACCTTCCCATTCAGCTTCAATG
AAGGGTACATCCGGGATGCTTATACGCCATTTCTAGAAATGACCAATGACAAG

Alignment

ORF - retro_pvam_158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.48 %
• Parental protein coverage: 89.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VEMLFRCNYLALVGGGK-KPKYPPNKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTF
          ..M.F.CN..ALV.GGK.K.KY.PN...I..DLKKK.VI..E.STEV..VKLR.DRI.V.LD...K.FT.
Retrocopy LQMAFCCNCFALVVGGK>KLKYFPNETLISNDLKKKVVIKTELSTEVEVVKLR*DRIMVILDPKTKMFTC

Parental  THNPHQLHVFETCYNPKGLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSCIALSL
          T...H.LHV.ETCYNP.GL.VLC.NS.NS.LA.PGTH..HVQLVDLAST...P.DIP......SCIALSL
Retrocopy TYSSHNLHVLETCYNPNGLYVLCHNSSNSFLALPGTHVCHVQLVDLASTKLLPMDIPTPKDIPSCIALSL

Parental  QGTRIATASEKGTLIRI-FDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAEDP-K
          ..T.....S.KGTL.RI.F.TSSG.LIQEL.R...AANIYCIN......LIC.S.DH.TVHI.A..DP.K
Retrocopy YRTEL--PSVKGTLTRI>FATSSGRLIQEL*R-CEAANIYCINQSR-CFLICISCDHSTVHISAVKDP>K

Parental  RNKQSSLASASFLPKYFSSKWSFSKFQVPSGSPCICAFGTEPNAVLAICADGS-YYKFLFNPKGECIRDV
          RN.Q.S..SA.FL.KYFSSK.S..KFQVPSGSPCI..FGT..N.V...CA.....Y.F.F......IRD.
Retrocopy RNEQYSFTSANFLVKYFSSK*SLPKFQVPSGSPCIRTFGTVSNTVISLCAAAA>LYTFPFSFNEGYIRDA

Parental  YAQFLEMTDDK
          Y..FLEMT.DK
Retrocopy YTPFLEMTNDK

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_158 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005657	1 retrocopy	retro_cpor_322,
Homo sapiens	ENSG00000141580	2 retrocopies	retro_hsap_1820, retro_hsap_1879,
Gorilla gorilla	ENSGGOG00000006132	2 retrocopies	retro_ggor_1376, retro_ggor_2173,
Macropus eugenii	ENSMEUG00000013344	1 retrocopy	retro_meug_233,
Macaca mulatta	ENSMMUG00000021803	1 retrocopy	retro_mmul_1330,
Mus musculus	ENSMUSG00000025173	1 retrocopy	retro_mmus_1487,
Nomascus leucogenys	ENSNLEG00000010516	1 retrocopy	retro_nleu_1227,
Pongo abelii	ENSPPYG00000008785	2 retrocopies	retro_pabe_150, retro_pabe_1559,
Pan troglodytes	ENSPTRG00000009807	3 retrocopies	retro_ptro_1171, retro_ptro_1262, retro_ptro_2912,
Pteropus vampyrus	ENSPVAG00000006212	1 retrocopy	retro_pvam_158 ,