RetrogeneDB ID: retro_pvam_500

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3489:817048..818071(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSPVAG00000010020
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 1 [Source:HGNC Symbol;Acc:9547]

Sequence

>retro_pvam_500
AAGGGATCAGATGCTGCCAGCAAACTGCCACTGGTGACACCTCACACTCAGTGCCAGTTAAAATTATTGAAGTTAGAATT
AAAGACTATCTTCCCATGGAGCAAGAATTCATTAGAAATAAGGAACAAATAAAGCCTTTAGAAGAAAAGCAAGAGGAGGA
AAGATCAAAGGCGGGTCATCTGAGGGGGACCCCAGTGTCGGTAGGAACCTTGGAAGAGACCATTGATGACAGTTACGCCA
TTCTGTCTACATCTGTGGGCTCAGAACATCACATCAGCATCCTTTTGTCTGTAGACAAGGATTTGCTGGAACCTGGCTGC
TCAGTCTTGCTCATCCACAAGGTGCATGCTGTGACAGGGGTGCTGATGGATGACACAGATCCCTTGGTCACAATGATGAA
GGTGAAAAAGTCCCCAGAGAAAGACCTATGCTGACATTATGAGGTTGGACAACCAAATCCAGAAAATTAAGAATCTGTGG
AGCTTCCTCTCAGTTATACTGAATATTATGAAGAGATGATCCCAAAGGGGTCATTCTCTATGGTCCACCTGGCACAGGCA
AAACCTTACTAGCCAAAGCAGTAGCAAACCAAACCTCAGCCACTTACTTGAGAATAGTTAGCTCTGCACTTATTTAGAGT
ACCTGGGCAATGGGCCCAAACTCATTGGATTGTTTCAGTGCTGTAGACAGCACATCGATCATGTTTTTCTGAAAAAATTG
ATACCATTGAGACAAAAAATATATGATTCATATCTGTGGTGAGAGAGAAATCAGCAAATGGCATGGAACCCGTTGAACCA
GTTGGATGAATTTGATTCAAAAGGAGACATGAATGTTATCACAGCCACAAACCGAATAGAAACTTTGACTCCAGCTCTTA
CCAGACCTGGCCGCATTGATAGGAAGATCGAGTTCCCTCTGCCTGACGAAAAGACCAAGAAGTGCACCTTTCAGATCTAC
ACAAGCAGAATGACGCTGGTTGATTACATGACACTGGACGACTTGATCATGGCTAGAGACGAA

Alignment

ORF - retro_pvam_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.47 %
• Parental protein coverage: 79.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KGPDAASKLPLVTPHTQCRL-KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSV
          KG.DAASKLPLVTPHTQC.L.K.....RIKDYL.ME.EFIRN.EQ.KPLEEKQEEERSK...LRGTP.SV
Retrocopy KGSDAASKLPLVTPHTQCQL<KIIEV-RIKDYLPMEQEFIRNKEQIKPLEEKQEEERSKAGHLRGTPVSV

Parental  GTLEEIIDDNHAIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKA
          GTLEE.IDD..AI.STSVGSEH..SIL..VDKDLLEPGCSVLL.HKVHAV.GVLMDDTDPLVT.MKV.K.
Retrocopy GTLEETIDDSYAILSTSVGSEHHISILLSVDKDLLEPGCSVLLIHKVHAVTGVLMDDTDPLVTMMKVKKS

Parental  PQ-ETYADIGGLDNQIQEIK-ESVELPLTHPEYYEEMGIKPPKG-VILYGPPGTGKTLLAKAVANQTSAT
          P...TYADI..LDNQIQ.IK.ESVELPL...EYYEEM....PKG.VILYGPPGTGKTLLAKAVANQTSAT
Retrocopy PE>KTYADIMRLDNQIQKIK<ESVELPLSYTEYYEEM---IPKG<VILYGPPGTGKTLLAKAVANQTSAT

Parental  FLRVVGSELI-QKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQ
          .LR.V.S.LI...YLG.GPKL...LF.....H....VF.........K.YDS....ER..Q......LNQ
Retrocopy YLRIVSSALI<LEYLGNGPKLI-GLFQCCRQHIDH-VFLKKLIPLRQKIYDSYLW*ERN-QQMAWNPLNQ

Parental  LDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIM
          LD.FDS.GD..VI.ATNRIETL.PAL.RPGRIDRKIEFPLPDEKTKK..FQI.TSRMTL.D..TLDDLIM
Retrocopy LDEFDSKGDMNVITATNRIETLTPALTRPGRIDRKIEFPLPDEKTKKCTFQIYTSRMTLVDYMTLDDLIM

Parental  AKDD
          A.D.
Retrocopy ARDE

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_500 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 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001839	4 retrocopies	retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris	ENSCAFG00000017510	2 retrocopies	retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni	ENSCHOG00000013595	1 retrocopy	retro_chof_1954,
Dasypus novemcinctus	ENSDNOG00000006458	1 retrocopy	retro_dnov_2162,
Equus caballus	ENSECAG00000003601	1 retrocopy	retro_ecab_355,
Echinops telfairi	ENSETEG00000002661	1 retrocopy	retro_etel_580,
Felis catus	ENSFCAG00000011310	8 retrocopies	retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
Myotis lucifugus	ENSMLUG00000007471	2 retrocopies	retro_mluc_2490, retro_mluc_508,
Macaca mulatta	ENSMMUG00000022990	1 retrocopy	retro_mmul_255,
Mustela putorius furo	ENSMPUG00000008150	4 retrocopies	retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus	ENSMUSG00000021178	3 retrocopies	retro_mmus_1517, retro_mmus_1826, retro_mmus_812,
Oryctolagus cuniculus	ENSOCUG00000006231	4 retrocopies	retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii	ENSOGAG00000032343	2 retrocopies	retro_ogar_3014, retro_ogar_367,
Pongo abelii	ENSPPYG00000025948	9 retrocopies	retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pteropus vampyrus	ENSPVAG00000010020	3 retrocopies	retro_pvam_1190, retro_pvam_350, retro_pvam_500 ,
Tursiops truncatus	ENSTTRG00000013582	1 retrocopy	retro_ttru_239,