RetrogeneDB ID: retro_pvam_703

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_848:15248..16418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRIM1
• Ensembl ID: ENSPVAG00000008017
• Aliases: None
• Description: primase, DNA, polypeptide 1 (49kDa) [Source:HGNC Symbol;Acc:9369]

Sequence

>retro_pvam_703
AAGCTTTATTACCAGAGGCTCCTATCCTACACCCAGTACTATCACTGGCTCAATTATGGTGGAATGATAAAGGATTACTT
TCAACACCATGCATTTTCATTCACAGTGAAAGATGATATTTACATTCACTACCAATTCTTCATCAACCAGAGCGATCTGG
AAAAGGGGATGCAGAAAATGAATCCATATAAGGTTGATATAGGCATGGTATATTCCCACAGACTCAATCAACACGATACA
GTGAAGCTGGGAGCTTTTCGGACTCAGAAAAAACTGATGTTTGATATTGACATGACAGACTGTGATGACGTGAGAAGAGG
TAGCAGTTCTGCAGACATGTGTTCTAAGTGCTAGACCTTCATGACAATGGCTGTACATATCATCGACCAAGCACTGAAGG
AAGCCTTGAGATTTAAGTGTCATGTCTGAATATATTCTGAAAGAAGAGGTGTTTGTTGTTGGGTCTGTGATGAATCAATT
AGAAAATAGTGCTCTGCAGCACATTCTGGGATAATTGAATATTTGAGTCTTGTAAAGCGTGGTTAAGGCATTAAAAAGAA
AGTTCACCTAAGTGAAAAAATCCACCCTTTTGTCAGAAAAATCTATAAACATAATAAATACTTTGAAGAATATGCCTTGG
TTGATCAAGATATTCTTGGAAATAAAGAAAGCTACAATAAGATTTTGGCCCTTGCTCCTGAAACAATTCATGATGACCTT
GAACAAGCCTTCCAAAAACATCACAGTTCACTTCAGCATTGAGAACATTTAAAGAAGGTAGCCAGATGTCTGAATAACAT
CGAAAGTGACAAATGTGGACCCTGGCTTGAGTGGAAGATTATGCTCCAGTACTGTTTTCCATGGCTAGATATTAATGTTA
GCAAAAGAATCAATGATTTGCTGAAGAGCCCTTTTAGTGTTCATCCTAAAATGGGTTGAATTTCGGTTTCTATTAATTAA
CAGAAAGTGGATCTGTTTGATCCATTTACTGTTCCAACTATAAGCTCCATCTGCCGTGAATTAGATGCCATTTCCACTAA
TGGAGAGGAAAAACAGAACAAAGCTGAGTCTATTATCAAACATAGAACTTGAGATTATAAAAAGACCAGTCTAGCTCCTG
ATGTAAAAGTTTTTGAAGTTTTTGGAAAACATGGAGAAATCTCGAAAAGG

Alignment

ORF - retro_pvam_703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.52 %
• Parental protein coverage: 93.79 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLYYRRLFPYAQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAV
          KLYY.RL..Y.QYY.WLNYGG.IK.YFQH..FSFT.KDDIYI.YQ.F.NQSDLEK.MQKMNPYK.DIG.V
Retrocopy KLYYQRLLSYTQYYHWLNYGGMIKDYFQHHAFSFTVKDDIYIHYQFFINQSDLEKGMQKMNPYKVDIGMV

Parental  YSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICSKCWTLMTMAIRIIDRALKEDFGFK
          YSHR.NQH.TVKLGAF..Q.K.L.FDIDMTD.DDVRR..SSAD.CSKC.T.MTMA..IID.ALKE...FK
Retrocopy YSHRLNQHDTVKLGAFRTQKK-LMFDIDMTDCDDVRRGSSSADMCSKC*TFMTMAVHIIDQALKEALRFK

Parental  HRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGPDVKKKVHLSEKIHPFVRKSINIINKYF
          .....YS.RRGV.CWVCDES.RK..SA..SGI.EYLSLVK.G...KKKVHLSEKIHPFVRK.I...NKYF
Retrocopy CHV*IYSERRGVCCWVCDESIRK*CSAAHSGIIEYLSLVKRG*GIKKKVHLSEKIHPFVRK-IYKHNKYF

Parental  EEYALVDQDIXXXXXXXXXXXXXXXXXIHDELQQSFQNHHSSLQRWEHLKKVARCLSNIKSDKYGPWLEW
          EEYALVDQDI.................IHD.L.Q.FQ.HHSSLQ..EHLKKVARCL.NI.SDK.GPWLEW
Retrocopy EEYALVDQDILGNKESYNKILALAPETIHDDLEQAFQKHHSSLQH*EHLKKVARCLNNIESDKCGPWLEW

Parental  EIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISSICHELDAISTIE
          .IMLQYCFP.LDINVSK.IN.LLKSPFSVHPK.G.ISV.I..QKVD.FDPFTVPTISSIC.ELDAIST..
Retrocopy KIMLQYCFPWLDINVSKRINDLLKSPFSVHPKMG*ISVSIN*QKVDLFDPFTVPTISSICRELDAISTNG

Parental  EEKGENKAESIIKHRTRDYKKTSLAPYVKVFEQFLENLDKSRK
          EEK..NKAESIIKHRT.DYKKTSLAP.VKVFE.F......S..
Retrocopy EEK-QNKAESIIKHRT*DYKKTSLAPDVKVFEVFGKHGEISKR

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_703 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703 ,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,