RetrogeneDB ID: retro_pvam_980

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_20369:9210..10052(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC13
• Ensembl ID: ENSPVAG00000008275
• Aliases: None
• Description: trafficking protein particle complex 13 [Source:HGNC Symbol;Acc:25828]

Sequence

>retro_pvam_980
ATTGATGATGTCATCCATGACAAAGTAATGAACATTGGAAGAACTGTCTCTGTGGGTTAAGTATCTATTCAACACAGTGT
GTAGGAAAGATGTTTTTTAGGAAACTCTGCTTATTTCCTTTCCTCCCACCACTAGAAGTTAAAACCAAGTTTTATAATTC
AGAGATGAGTGACTTATTTCTTGAAGTACAGATTCAGAATATTTCATCTTCAACTGTTTTTATAAAAAAGGTTTCCGTAG
AACCATCTGAAATGTACACTGGGGAAGAATTAAATACTGTCAATCAGGCTGGAGAAGATGAGTGTACCTTTGGAACAAGA
ACATTTTTGCAGTCAATGGAAGGACGCCAGTATTTGTACCACTTTCAGACCAAGAAGGAATTTTTAGAGAAATTTGGTAT
CATTAGAGGACTAACAAAAATGGGAAAATTGGATATAGTGTGGAAAAGAAATTTAGGTGAAATGGCTATGCTACAGACAA
TCCAACTTGAAAGAGAGGCTCCAAGTTATGGAAACATGATGCTGTCTCTGGAGACAATCCCAGATACTGTAATTCTAGAA
GAGCCTTTTCATATTACCTGTAAGATAACAAACTGCAGTAATAGGAAAATGAAATTGGTTTTGAAGATGTGTGATACAGA
TTCTATTCGTTGGTGTGGAAGCTCAGGAAGGAACCTTGGGAAGCTGTCTCCAAGTTCATCTTTCCACTTTACCCTGGCAC
TACTGTCCTTAAAAATGGGCCTTCAAAGTGTCTCTGGCATACGGATAACAGACAAATTATTAAAGAAAACCTATGTCTGT
GATGATGTTGCAAAAGTCTGTGTAATACCTTCCATATTAAAA

Alignment

ORF - retro_pvam_980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 80.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDDVIHHEVKEIGTHILVCAVS-YTTQGGEKMYFRKFFKFQVLKPLDVKTKFYNAEVSITDEVFLEAQIQ
          IDDVIH..V..IG....V..VS.Y.TQ...KM.FRK...F..L.PL.VKTKFYN.E.S.....FLE.QIQ
Retrocopy IDDVIHDKVMNIGRTVSVG*VS<YSTQCVGKMFFRKLCLFPFLPPLEVKTKFYNSEMS---DLFLEVQIQ

Parental  NITTSPMFMEKVSLEPSIMYNVAELNSVNQAGECVTTFGTRTYLQPMDTRQYLYCLKPKKEFAEKAGIIK
          NI..S..F..KVS.EPS.MY...ELN.VNQAGE...TFGTRT.LQ.M..RQYLY....KKEF.EK.GII.
Retrocopy NISSSTVFIKKVSVEPSEMYTGEELNTVNQAGEDECTFGTRTFLQSMEGRQYLYHFQTKKEFLEKFGIIR

Parental  GVTVIGKLDIVWKTNLGERGRLQTSQLQRMAPGYGDVRLSLEAIPDTVNLEEPFHITCKITNCSERTMDL
          G.T..GKLDIVWK.NLGE...LQT.QL.R.AP.YG...LSLE.IPDTV.LEEPFHITCKITNCS.R.M.L
Retrocopy GLTKMGKLDIVWKRNLGEMAMLQTIQLEREAPSYGNMMLSLETIPDTVILEEPFHITCKITNCSNRKMKL

Parental  VLEMCNTNSIHWCGISGRQLGKLHPSSSLCLALTLLSSVQGLQSISGLRLTDTFLKRTYEYDDIAQVCVV
          VL.MC.T.SI.WCG.SGR.LGKL.PSSS....L.LLS...GLQS.SG.R.TD..LK.TY..DD.A.VCV.
Retrocopy VLKMCDTDSIRWCGSSGRNLGKLSPSSSFHFTLALLSLKMGLQSVSGIRITDKLLKKTYVCDDVAKVCVI

Parental  SSAIK
          .S..K
Retrocopy PSILK

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_980 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006026	1 retrocopy	retro_chof_1834,
Dasypus novemcinctus	ENSDNOG00000006386	1 retrocopy	retro_dnov_1288,
Equus caballus	ENSECAG00000011983	1 retrocopy	retro_ecab_1074,
Pteropus vampyrus	ENSPVAG00000008275	1 retrocopy	retro_pvam_980 ,
Sorex araneus	ENSSARG00000000639	1 retrocopy	retro_sara_394,
Ictidomys tridecemlineatus	ENSSTOG00000021318	1 retrocopy	retro_itri_1455,
Tarsius syrichta	ENSTSYG00000004582	1 retrocopy	retro_tsyr_18,
Tursiops truncatus	ENSTTRG00000006537	1 retrocopy	retro_ttru_1068,