RetrogeneDB ID: retro_pvam_629

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_427:13576..14129(+)
• Located in intron of: ENSPVAG00000017778

Retrocopy information

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

Parental gene information

• Parental gene symbol: C18orf21
• Ensembl ID: ENSPVAG00000009174
• Aliases: None
• Description: chromosome 18 open reading frame 21 [Source:HGNC Symbol;Acc:28802]

Sequence

>retro_pvam_629
TGGGCCAGGCCCACTATCTCTTATACTAAAAGCACTTTTGAAGGAACATGTCCACACTGTTTCCAGTTGCTGGTTCTGGA
TAACTCTCGAGTGTACCTCAAACCCAAGCCCAAACTGACACCCAAAATACAGAAACTTCTTAACTGAGAAGCAAGAAATT
ATACAGTTTTAAAGAAGCAATTGTGGAAAAATACAAAGACTCCAAAATTGTATTGTTTATTACTTGTAAAACATGCAACA
AAACAGTTAAACATCATGGTAAAAGCAGAAGCTTTCTATCAGCACTGAAGAGCAATCCTACCACACCTATGAGTAAACTC
AGCCTGAAGGCACCAGAGAGACTCTTAAGTTCTACAACCTAAATCATGACATGTCTCATTCCAAAGGCAAGAAGAGCCCA
GTATTGATTTTCAGAACACTAACATCTGGACAGTCAACACTCACTCAAAGAATGCTAACAAAGAAAGAAACACTTCTCTC
AACTAAAAATGTTGCTTAGAGTAAATCCCAAAAGAATCCAAAAGTGGACTTGAGAAATTTCTTATCTTCTTTG

Alignment

ORF - retro_pvam_629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.62 %
• Parental protein coverage: 86.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WAYSSTHDAKSTFEGTCPYCFQLLVLDNYRVRLK-PKPKLTPRIQKLLN-REARNYTLSFKEAKIVEKYK
          WA.......KSTFEGTCP.CFQLLVLDN.RV.LK.P.P...P.....L..R....Y..SFKEA.IVEKYK
Retrocopy WARPTISYTKSTFEGTCPHCFQLLVLDNSRVYLK>PSPN*HPKYRNFLT>RSKKLY--SFKEA-IVEKYK

Parental  DSKSVLLITCKTCNRTVKHHGKSRSFLSALKSNPTTPTSKLSLKTPERKTLSSA-DLNHDVSGSKG-KSP
          DSK.VL.ITCKTCN.TVKHHGKSRSFLSALKSNPTTP.SKLSLK.PER..LSS...LNHD.S.SKG.KSP
Retrocopy DSKIVLFITCKTCNKTVKHHGKSRSFLSALKSNPTTPMSKLSLKAPER-LLSST<NLNHDMSHSKGKKSP

Parental  ALIFRTPTSGQSTPTCSSKNTSKTKKRFSQLKMLLSQSESQKSPKVDFRNFLSSL
          .LIFRT.TSGQST.T.......K.....S......S.S...K.PKVD.RNFLSSL
Retrocopy VLIFRTLTSGQSTLT--QRMLTKKETLLSTKNVA*SKSQ--KNPKVDLRNFLSSL

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_629 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029548	1 retrocopy	retro_cfam_1636,
Callithrix jacchus	ENSCJAG00000021041	2 retrocopies	retro_cjac_1030, retro_cjac_2169,
Cavia porcellus	ENSCPOG00000025449	1 retrocopy	retro_cpor_1461,
Felis catus	ENSFCAG00000000626	1 retrocopy	retro_fcat_1717,
Homo sapiens	ENSG00000141428	1 retrocopy	retro_hsap_3062,
Gorilla gorilla	ENSGGOG00000026334	1 retrocopy	retro_ggor_2102,
Macaca mulatta	ENSMMUG00000018782	1 retrocopy	retro_mmul_1876,
Monodelphis domestica	ENSMODG00000025605	1 retrocopy	retro_mdom_260,
Mus musculus	ENSMUSG00000024273	2 retrocopies	retro_mmus_1676, retro_mmus_610,
Nomascus leucogenys	ENSNLEG00000006237	1 retrocopy	retro_nleu_1655,
Oryctolagus cuniculus	ENSOCUG00000028046	2 retrocopies	retro_ocun_1910, retro_ocun_435,
Ochotona princeps	ENSOPRG00000011163	2 retrocopies	retro_opri_1222, retro_opri_283,
Pongo abelii	ENSPPYG00000009110	1 retrocopy	retro_pabe_2536,
Pan troglodytes	ENSPTRG00000009973	2 retrocopies	retro_ptro_1981, retro_ptro_2935,
Pteropus vampyrus	ENSPVAG00000009174	3 retrocopies	retro_pvam_1086, retro_pvam_1488, retro_pvam_629 ,
Tupaia belangeri	ENSTBEG00000016670	1 retrocopy	retro_tbel_4056,
Tarsius syrichta	ENSTSYG00000010817	2 retrocopies	retro_tsyr_1675, retro_tsyr_1787,