RetrogeneDB ID: retro_pvam_317

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2498:709909..710759(-)
• Located in intron of: ENSPVAG00000000216

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENO1
• Ensembl ID: ENSPVAG00000005030
• Aliases: None
• Description: enolase 1, (alpha) [Source:HGNC Symbol;Acc:3350]

Sequence

>retro_pvam_317
ATGGCTACTTTCAGATTCCATGTCAGGGACTTTAGACTATTGTGGGGATCCAACTATTGAGGTAACTGCCTTACTCTTAA
AAGGTTCTTTAGACCTGCCATGGCCCAGAGGTGCCTCAACTAGTCTCTTTGAGGTCCTAAAGCTCCGGAACGATGACAAG
ATTTGATATATAGGTAAAAATGTCTCAAAGGCTGTCAAGCACATCAATAAAATCATTGCACCTGCCCCAAGTAGCAAGAA
ACTGAATTTTATGAAATAGGATTTTGACAAACTGATGCTAGGGATGAATGGCACGGAGACTAAATCTAAATTTGGTGTAC
ACGCCATAATAGGGTGTCCCTATGCTGTCTATAAGGCTGAAGATGCTGAGAAGGGGGCTTCCTGAACTGTCACACTGCTG
ACTTGATTGGCACTTCTGAAGTCATCCTGTAAGTTGCAGTTTTAATGTGGTTGGTGGTAGTTCTCACACCGGCAACTCGG
TGACAATGCAGAAGTGGTCCTCCCTGCTGATGCAGCAGACTTCAGGGAAGCCATGTCTGTTGGAGCTGAGGTTTAGCACA
AGCTGGAAGAATGGTATTAAGAAGAAATAGGGAAAGCTGCTACCAATGAGGGGAATGAAGAGGGCTTTGCTCCTAACATC
CTAGAGATTAAGTAAGCCTCAGAGCTTCTAAAGCATGCAATTGTGAAAGCCAGCTACACAAATAAGATTGTAATTGACAC
AGATGTGGCTGCCTCTGAGTTCTTCAGGTCTGGGAGGTATGACTTGGACTTTAAGTCTCCTGATGACCCCAGCAGGTACA
TCTTTCCTGACTAGCAAGTGACCCTGTACATGTCCTCCATTAAGGACTGG

Alignment

ORF - retro_pvam_317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.9 %
• Parental protein coverage: 66.05 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSILKIHARIF-DSRGNPTVEVDLCTSKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSKAVEHIN
          M.....H.R.F.D..G.PT.EV.....KG......P.GAST...E.L.LR..DK..Y.GK.VSKAV.HIN
Retrocopy MATFRFHVRDF>DYCGDPTIEVTALLLKGSLDLPWPRGASTSLFEVLKLRNDDKI*YIGKNVSKAVKHIN

Parental  KTIAPALVSKKLNVTEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVP-LYRHIADLAG
          K.IAPA..SKKLN.......DKLM..M.GTE.KSKFG..AI.G...AV.KA...EKG...L..H.ADL.G
Retrocopy KIIAPAPSSKKLNFMK*D-FDKLMLGMNGTETKSKFGVHAIIGCPYAVYKAEDAEKGAS<LNCHTADLIG

Parental  NSEVILPVP-AFNVINGGSH-AGNKLAMQEFMILPVGAANFTEAMRIGAEVYHNLKNVIKEKYGKDATNV
          .SEVIL.V...FNV..GGS......L.......LP..AA.F.EAM..GAEV.H.L.....E..GK.ATN.
Retrocopy TSEVIL*VA<SFNVV-GGSS<SHRQLGDNAEVVLPADAADFREAMSVGAEV*HKLEEWY*EEIGKAATNE

Parental  GDEGGFAPNILENKEALELLKNAIGKAGYTDKVVIGMDVAASEFFRSGKYDLDFKSPDDPSRYITPDQLA
          G.E.GFAPNILE.K.A.ELLK.AI.KA.YT.K.VI..DVAASEFFRSG.YDLDFKSPDDPSRYI.PD...
Retrocopy GNEEGFAPNILEIK*ASELLKHAIVKASYTNKIVIDTDVAASEFFRSGRYDLDFKSPDDPSRYIFPD*QV

Parental  DLYKSFIKDY
          .LY.S.IKD.
Retrocopy TLYMSSIKDW

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_317 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 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Pteropus vampyrus	ENSPVAG00000005030	1 retrocopy	retro_pvam_317 ,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,