RetrogeneDB ID: retro_pvam_1019

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_22918:2536..3525(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA4A
• Ensembl ID: ENSPVAG00000010798
• Aliases: None
• Description: tubulin, alpha 4a [Source:HGNC Symbol;Acc:12407]

Sequence

>retro_pvam_1019
GTAAGGGGTGATGACTCCTTCAGTACCCTCTTCAGTGATACAGGCACTGGCAAGCATGTGCCCAGGGCAGTGTTTGTAGA
CCTGGAACCCACAGTCATTCATGAAGTTTGTGCTGGCACCTACTGCCAGCTCTTCTACCCTGAGCAGCTTACCACAGGCA
AGGAAGATGCTGCCCATAACTTTGCTTGTAGGTACTTGTCCATTGGCAAGGAGATCATTGATTGACCTTGTCTTGGACCA
CATTCGGAAGCTGGCTGACCAGTGTACAGGTCTTCAGGGCTTCTTGGTTTTCCGTAGCTTTGGTGGGAGAACTGGTTCTG
GGTTCACATCCCTGCTCATGGAATATCTCTCTGTTGATTATGACAGGAAGTCCATGCTGGAGTTCTCCATTTACCCAGCC
CCTCAGATTTCCACAGCTGTAGTTGAGCACTACTAATCCAGCCTCACCACCCTCACTACCCTGAAGCACTCTGCATTCAT
GGTTGAAAATGAGGCCATCTATGACATCTGTCATAGGAACTTTTTTATATTGAGCACCAACCTATGCTAACCTGAATAGA
TTGATTAGTCGCATTGTATCCTCCATCACTGTTTCCCTGAGATTTAATGGTGCCCGAATATTGATGTGACAGAATTCCAG
ACCAGCCTGGTGCCCTATCCCTGCATCCACTCCCCTCTGGCCACATATGACCCTGTCATCCCTGCTGAGAAAGACTACCA
TGAATAGCTTTCTGTAGCAGAGATCACCAGTGCATGCTTTAAGCACATATCACACATGGTGAAATGTGACCCTCACCACT
GTAAATACATGGCTTGCTGTCTCTTGTACCATGGGTTACGTGGTTCCCAAAGATGTCAATACTGCCATTGCCACCATCAA
GACCGAGTGTACTATCCAGTTTGTGGACTAGTGCCCCACTGTCTTCAAAGATGGCATTAATTACTAGCCTCCCACTGTAG
TACTTGGTGGAGACCGAGCCAAAGTACAA

Alignment

ORF - retro_pvam_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.03 %
• Parental protein coverage: 74.32 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IGGGDDFTTFFCETGAGKHVPRAVFVDLEPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGK
          ..G.D.F.T.F..TG.GKHVPRAVFVDLEPTVI.E...G.Y.QLF.PEQL.TGKEDAA.N.A.....IGK
Retrocopy VRGDDSFSTLFSDTGTGKHVPRAVFVDLEPTVIHEVCAGTYCQLFYPEQLTTGKEDAAHNFACRYLSIGK

Parental  EIID-PVL-DRIRKLSDQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
          EIID.P.L.D.IRKL.DQCTGLQGFLVF.SFGG.TGSGFTSLLME.LSVDY..KS.LEFSIYPAPQ.STA
Retrocopy EIID*PCL>DHIRKLADQCTGLQGFLVFRSFGGRTGSGFTSLLMEYLSVDYDRKSMLEFSIYPAPQISTA

Parental  VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIE-RPTYTNLNRLISQIVSSITASLRFDGAL-
          VVE.Y.S.LTT.TTL.HS..AFMV.NEAIYDIC.RN..I...PTY.NLNRLIS.IVSSIT.SLRF.GA..
Retrocopy VVEHY*SSLTTLTTLKHS--AFMVENEAIYDICHRNFFIL>APTYANLNRLISRIVSSITVSLRFNGAR<

Parental  NVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLL
          N.D.TEFQT.LVPYP.IH.PLATY.PVI.AEK.YHE.LSVAEIT.ACF.....MVKCDP.H.KYMACCLL
Retrocopy NIDVTEFQTSLVPYPCIHSPLATYDPVIPAEKDYHE*LSVAEITSACFKHISHMVKCDPHHCKYMACCLL

Parental  YR-GDVVPKDVNAAIAAIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQ
          Y..G.VVPKDVN.AIA.IKT...IQFVD.CPT.FK.GINY.PPTVV.GGD.AKVQ
Retrocopy YH>GYVVPKDVNTAIATIKTECTIQFVD*CPTVFKDGINY*PPTVVLGGDRAKVQ

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_1019 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Dipodomys ordii	ENSDORG00000000154	3 retrocopies	retro_dord_460, retro_dord_564, retro_dord_786,
Echinops telfairi	ENSETEG00000010296	2 retrocopies	retro_etel_1816, retro_etel_1993,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Microcebus murinus	ENSMICG00000000804	1 retrocopy	retro_mmur_103,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Pteropus vampyrus	ENSPVAG00000004646	1 retrocopy	retro_pvam_929,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019 ,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Ictidomys tridecemlineatus	ENSSTOG00000019497	1 retrocopy	retro_itri_203,
Tursiops truncatus	ENSTTRG00000010042	1 retrocopy	retro_ttru_531,