RetrogeneDB ID: retro_pvam_35

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1088:19431..20072(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPS2
• Ensembl ID: ENSPVAG00000005052
• Aliases: None
• Description: G protein pathway suppressor 2 [Source:HGNC Symbol;Acc:4550]

Sequence

>retro_pvam_35
GTGCCTGCGTCCCTGGAGCGCCCCAGGCTTTCCAGCGCCATGGCCAGGGCGTTGCACATCGTGATGGAGCAAGGGTGCAA
GGGGCAGGGGGAAGAAGAAGTGGACGAGACGATGGAACAGAAGACGAAGGAAGAGCGGGAGGGAAGGAAGGAAAAAGAGA
TGGAAGAGAGAACGTCACTGGAGGAGACCAGGGGACAAATCCTGAAAGTGCACGAGAAGCTTTTGGCCCTGCAGGGAGAG
AAGCACCGGCTTTTCCTGCAGCTCGAGAAAGTTTCCCACGAGGAAGAAAAACAGAAGCGAAAGGAGCAGAGTGACCCGAC
CTGACATCAGCGGCGAACCCGCAGGCCTGGCCGTCCACACGGGAATTCGCCTGCTCGGCGTGCAGGGGAGCCCCGGAGGG
CAAGAGTCGCCCGGGGAACCTCGGGGCAGCGGACAGAGCCAAACAGATGTTCACACCCCAAGGGCTTACAACCCAGCACT
GCGTGGGCTCAGCAGCCGCTTTCCCAGAGACCCCAGAGCACGGGCAAGATCGAGGCAGCACCTATGGGACGGCTCAGCCC
CCACCTCGCTATGGGCCCCCTCAACCCACCTAGAGTCCTAGTCAGCAGCTCAGAGCACCCTCAGCGGTTCCTGCCGCGCG
G

Alignment

ORF - retro_pvam_35 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.16 %
• Parental protein coverage: 67.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPALLERPKLSNAMARALHRHIMMERERKRQEEEEVDKMMEQKMKEEQERRKKKEMEERMSLEETKEQIL
          .PA.LERP.LS.AMARALH..I.ME...K.Q.EEEVD..MEQK.KEE.E.RK.KEMEER.SLEET..QIL
Retrocopy VPASLERPRLSSAMARALH--IVMEQGCKGQGEEEVDETMEQKTKEEREGRKEKEMEERTSLEETRGQIL

Parental  KLQEKLLALQEEKHQLFLQLKKVLHEEEKRRRKEQSDLTT-LTSAAYPQS-LTVHTGTHLLSMQGSPGGH
          K..EKLLALQ.EKH.LFLQL.KV.H.EE...........T.LTSAA.PQ..L.VHTG..LL..QGSPGG.
Retrocopy KVHEKLLALQGEKHRLFLQLEKVSH-EEEKQKRKEQSDPT<LTSAANPQA<LAVHTGIRLLGVQGSPGGQ

Parental  -NRPGTLMAADRAKQMFGPQVLTTRHYVGSAAAFAGTPEHGQFQGSPGGAYGTAQPPPHYGPTQPTYSPS
          ..RPG.L.AADRAKQMF.PQ.LTT.H.VGSAAAF..TPEHGQ..GS....YGTAQPPP.YGP.QPT.SPS
Retrocopy >SRPGNLGAADRAKQMFTPQGLTTQHCVGSAAAFPETPEHGQDRGS---TYGTAQPPPRYGPPQPT*SPS

Parental  QQLRAPSAFPAVQ
          QQLRAPSA.PA..
Retrocopy QQLRAPSAVPAAR

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_35 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016576	2 retrocopies	retro_amel_1236, retro_amel_362,
Equus caballus	ENSECAG00000010635	2 retrocopies	retro_ecab_124, retro_ecab_480,
Homo sapiens	ENSG00000132522	2 retrocopies	retro_hsap_2738, retro_hsap_4222,
Gorilla gorilla	ENSGGOG00000001672	1 retrocopy	retro_ggor_1907,
Macropus eugenii	ENSMEUG00000010645	2 retrocopies	retro_meug_1327, retro_meug_182,
Myotis lucifugus	ENSMLUG00000026169	1 retrocopy	retro_mluc_1045,
Mus musculus	ENSMUSG00000023170	1 retrocopy	retro_mmus_1476,
Nomascus leucogenys	ENSNLEG00000009364	2 retrocopies	retro_nleu_2477, retro_nleu_600,
Pan troglodytes	ENSPTRG00000023046	1 retrocopy	retro_ptro_1852,
Pteropus vampyrus	ENSPVAG00000005052	1 retrocopy	retro_pvam_35 ,
Sus scrofa	ENSSSCG00000017940	1 retrocopy	retro_sscr_742,