RetrogeneDB ID: retro_pvam_1356

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_6812:60970..62278(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000007982
• Aliases: None
• Description: None

Sequence

>retro_pvam_1356
GATGAGGATCAAGCCCTGGAGGACTGGATGTCCTCAGAGACATCTGCCCTGCCCCATCCTCGCTGGAAAGTCCTTACTGC
TCTTCGAGAGCGGCAGCTGGGTTCAAGTCCCCGCTTTGTATATGAGGCCTGTGGGGCAAGAGTCTTTGTGCAGCGTTTCC
ATCTGCAGTATGGGCTTGAAGGCCATGGTGGTTGTGTCAATTGCGCGCACTTTAACCAGCGTGGTACCTTGCTGGCCAGT
AGCAGTGATGACCTTAGAGTGATACTTTGGGATTGGATGCGTAAGCAGCCAGTACTGGACTTTGAGACTGGTCACAAAAA
TAACGTCTTTCAGGCCAAGTTCCTTCCCAACTGTGGTGATTCCACCCTGGTCACATGTGCCCGTGATGGGCAGATACGGG
TAACAGACCTAAATGCTCTGCCACACCTTAATCTTTCCAAGTGTGTGGCCCAGCATAAGGGAGCCTGCCACAAGATGGCT
CTGGAGCCAGACTCCCCTTTTAAGTTCCTAACTTCAGGTGAAGATGCAGTTGTCTTTGGCATTGACCTCAGACGAAGCCA
GCCAGCTTCAAAATTGGTGGTAACAAAAGAGAAGGAGATGAAAGTAGGACTGTACTCAATCTTTGTGAATCCCATGAATA
CTTACCAGTTTGCTGTGGGTGGACAAGATCAGTTTGTTAGAATTTATGACCAGAGGAAAATTGACGAGAATGAGAATAAT
GGAGTATTTAAGAAATTCTGTCCTCATCACCTGATCGGCCATGATTCCAAAGCAGCCATCACCTGCCTCATGTACAGCCA
TGATGGCACAGAGCTCCTGGCCAGTTACAATGATGAAGATATTTACCTCTTTAACTCCTCTCACTGTGATGGAGCCCAGT
ATGTTAAGAGATATAAGGGGCACAGAAATTATGCCACGGTCAAAGGCGTCAGTTTCTATGGCCCTAGAAGTGAGTTTGTG
GTGAGCGGTAGCGATTGTGGGCACATCTTCCTCTGGGAAAAATCATCTTGCCAGATCATTCAGTTCATGAACGGGGACAG
GACAGGAACCATAAACTGTCTTGAGCCCCACCCTCACCTACCTGTGATGGCGACCTGTGGCCTAGACCATGATGTCAAGA
TCTGGGCACCCACAGCTAAAGCTACCACAGAGCTTACTGGATTAAAGAATGTTGTTAAGAAGAACAAGCGGGAACGAGAT
GAAGATAGAATGCACCGTACTTACCTGTTTGACGACCACATGATTTGGTTCCTCATGCATCACCTGACACAGAGAGATCA
TCACCGGCACTGGGGAGATCCTGAAATC

Alignment

ORF - retro_pvam_1356 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.36 %
• Parental protein coverage: 73.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDERALEDWVSSETSALPRPRWQALPALRERELGSSARFVYEACGARVFVQRFRLQHGLEGHTGCVNTLH
          D...ALEDW.SSETSALP.PRW..L.ALRER.LGSS.RFVYEACGARVFVQRF.LQ.GLEGH.GCVN..H
Retrocopy DEDQALEDWMSSETSALPHPRWKVLTALRERQLGSSPRFVYEACGARVFVQRFHLQYGLEGHGGCVNCAH

Parental  FNQRGTWLASGSDDLKVVVWDWVRRQPVLDFESGHKSNVFQAKFLPNSGDSTLAMCARDGQVRVAELSAT
          FNQRGT.LAS.SDDL.V..WDW.R.QPVLDFE.GHK.NVFQAKFLPN.GDSTL..CARDGQ.RV..L.A.
Retrocopy FNQRGTLLASSSDDLRVILWDWMRKQPVLDFETGHKNNVFQAKFLPNCGDSTLVTCARDGQIRVTDLNAL

Parental  QCCKNTKRVAQHKGASHKLALEPDSPCTFLSAGEDAVVFTIDLRQDRPASKLVVTKEKEKKVGLYTIYVN
          ......K.VAQHKGA.HK.ALEPDSP..FL..GEDAVVF.IDLR...PASKLVVTKEKE.KVGLY.I.VN
Retrocopy PHLNLSKCVAQHKGACHKMALEPDSPFKFLTSGEDAVVFGIDLRRSQPASKLVVTKEKEMKVGLYSIFVN

Parental  PANTHQFAVGGRDQFVRIYDQRKIDENENNGVLKKFCPHHLVNSESKANITCLVYSHDGTELLASYNDED
          P.NT.QFAVGG.DQFVRIYDQRKIDENENNGV.KKFCPHHL....SKA.ITCL.YSHDGTELLASYNDED
Retrocopy PMNTYQFAVGGQDQFVRIYDQRKIDENENNGVFKKFCPHHLIGHDSKAAITCLMYSHDGTELLASYNDED

Parental  IYLFNSSHSDGAQYVKRYKGHRNNATVKGVNFYGPKSEFVVSGSDCGHIFLWEKSSCQIIQFMEGDKGGV
          IYLFNSSH.DGAQYVKRYKGHRN.ATVKGV.FYGP.SEFVVSGSDCGHIFLWEKSSCQIIQFM.GD..G.
Retrocopy IYLFNSSHCDGAQYVKRYKGHRNYATVKGVSFYGPRSEFVVSGSDCGHIFLWEKSSCQIIQFMNGDRTGT

Parental  VNCLEPHPHLPVLATSGLDHDVKIWAPTAEASTELTGLKDVIKKNKRERDEDSLHHTDLFDSHMLWFLMH
          .NCLEPHPHLPV.AT.GLDHDVKIWAPTA.A.TELTGLK.V.KKNKRERDED..H.T.LFD.HM.WFLMH
Retrocopy INCLEPHPHLPVMATCGLDHDVKIWAPTAKATTELTGLKNVVKKNKRERDEDRMHRTYLFDDHMIWFLMH

Parental  HLRQRRHHRRWREPGV
          HL.QR.HHR.W..P..
Retrocopy HLTQRDHHRHWGDPEI

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_1356 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014293	1 retrocopy	retro_amel_47,
Bos taurus	ENSBTAG00000005796	1 retrocopy	retro_btau_1853,
Canis familiaris	ENSCAFG00000031010	1 retrocopy	retro_cfam_223,
Callithrix jacchus	ENSCJAG00000005913	1 retrocopy	retro_cjac_1322,
Echinops telfairi	ENSETEG00000012876	1 retrocopy	retro_etel_654,
Felis catus	ENSFCAG00000003925	1 retrocopy	retro_fcat_14,
Mustela putorius furo	ENSMPUG00000013949	1 retrocopy	retro_mputfur_173,
Mus musculus	ENSMUSG00000026554	1 retrocopy	retro_mmus_111,
Otolemur garnettii	ENSOGAG00000011349	1 retrocopy	retro_ogar_2113,
Pteropus vampyrus	ENSPVAG00000007982	1 retrocopy	retro_pvam_1356 ,
Sus scrofa	ENSSSCG00000006388	1 retrocopy	retro_sscr_88,
Tupaia belangeri	ENSTBEG00000001566	1 retrocopy	retro_tbel_3644,