RetrogeneDB ID: retro_pvam_401

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2940:314315..315509(-)
• Located in intron of: ENSPVAG00000007171

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT20H
• Ensembl ID: ENSPVAG00000014609
• Aliases: None
• Description: suppressor of Ty 20 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20596]

Sequence

>retro_pvam_401
CAGCGAGCTTTAGAGCAAGCTTTGGATCGTGCGGACTATGTCATTGAAAGCGCCCAACAGAGACCCCCTAAAAGGAAATA
CTCATCTAGTGGGAGACAAACTCTCTATGAAAAGCTGTATGACATATATGTTGAAGAATGTGGGAAAGAGCCCGAGATTA
CGGAGGAATTAACGAGCAATGTGAACTTGTTAGAGAAGCTCATTAAGAGAGAGTCATTGCCGTGTTTAGTAGTCAACCTG
TACCCAGGAAGGGAGGGCTATTCGCTGATGCTCAAGGGAAAAAATGGTTATTTGGAGACCGTTCAATTGCCTTATGAAGA
AGGAGAATTACTTGAATACATGGATGCAGAAGAATTACCTCCTATTTTGGTGGATATCCTGGAAAGTGCTCCAGTTAACC
TTTTTCACTGTGGGTGTGTCATAACAGAAATACGGGACTATAGGCAGTGCAGTAATACGGAAGGCCCCCGTTACCAGAGC
AGGCACATTCTCTTACGTCCAACGATGCAGACGTTAGCTTGTGATGTACAGTCCATAACCAGCGATAACCAGACATGGAC
CCAGGATGACAAACTTTTGCTCGAGAGCCAGCTGATCTTGGCTACAGCCGAACCACTGTGTCTTGACCCCTCTATATCAG
TAGCCTGCGCCGAAAACAGGCTGCTCTTTAACAGGCAAAAGATGAACACTCACCCGATGAGAAGGAACTTCAAGCGGTAT
TCTACAGCCTCCCTGAATCGCGAGCAGGAGCTGCCTCATCATCGTTCACTCTCTCCTGAGCTAAGAGTATGGTCTTCTTG
CAAAAGAATCAGAGAAAGTCAAGCAAGTCAGCAGTATGACCTCAAAATTACCAAAGCAAATTGTGTAGATATGTGGAAAC
GGCGGCCCTGTGAGTTGGCGGTCCCTTCTGAAGTGGATGTGTTGAAATACGCTAAAGGGAAGAGGTCTGTCCAATGTGAT
GACTCACAACCAACAGTCTGGCCAGACCTCGAGCTAAGAGATGATTCTTTGTATGGATATGAAGCCAGCGATCAGTCCCA
GGCAACAAAGCAGATCTTCCTGCAGTCACTTAATGATCCATTTATCTCTGGAAAAAGGCCATGTAAAACATCCAGATGCC
TGAGACATATGACTCCCCACCACTCCTCCACAGATGACCATTTGAGTAGTTTCCTGCCTTGGTTAAAGACTGAT

Alignment

ORF - retro_pvam_401 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.42 %
• Parental protein coverage: 51.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQALELALDRAEYVIESARQRPPKRKYLSGGRKSVFQKLYDLYIEECEKEPEV-KKLRRNVNLLEKLVMQ
          Q.ALE.ALDRA.YVIESA.QRPPKRKY.S.GR.....KLYD.Y.EEC.KEPE....L..NVNLLEKL...
Retrocopy QRALEQALDRADYVIESAQQRPPKRKYSSSGRQTLYEKLYDIYVEECGKEPEITEELTSNVNLLEKLIKR

Parental  ETLSCLVVNLYPGNEGYSLMLRGKNGSDSETIRLPYEEGELLEYLDAEELPPILVDLLEKSQVNIFHCGC
          E.L.CLVVNLYPG.EGYSLML.GKNG...ET..LPYEEGELLEY.DAEELPPILVD.LE...VN.FHCGC
Retrocopy ESLPCLVVNLYPGREGYSLMLKGKNGY-LETVQLPYEEGELLEYMDAEELPPILVDILESAPVNLFHCGC

Parental  VIAEIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSITSDNHKWTQEDKLLLESQLILATAEPLCLD
          VI.EIRDYRQ.SN...P.YQSRHILLRPTMQTL.CDV.SITSDN..WTQ.DKLLLESQLILATAEPLCLD
Retrocopy VITEIRDYRQCSNTEGPRYQSRHILLRPTMQTLACDVQSITSDNQTWTQDDKLLLESQLILATAEPLCLD

Parental  PSITVTCTANRLLYNKQKMNTRPMKRCFKRYSRSSLNRQQDLSHCPP-PPQLKLLDFLQKRKERKAGQHY
          PSI.V.C..NRLL.N.QKMNT.PM.R.FKRYS..SLNR.Q.L.H.....P.L..........E..A.Q.Y
Retrocopy PSISVACAENRLLFNRQKMNTHPMRRNFKRYSTASLNREQELPHHRSLSPELRVWSSCKRIRESQASQQY

Parental  DLKISKAGNCVDMWKRNPCNLAIPSEVDVEKYAKVEKSIKSDDSQPTVWPAHDIKDDYVFECEAGNQYQK
          DLKI.KA.NCVDMWKR.PC.LA.PSEVDV.KYAK...S...DDSQPTVWP.....DD.....EA..Q.Q.
Retrocopy DLKITKA-NCVDMWKRRPCELAVPSEVDVLKYAKGKRSVQCDDSQPTVWPDLELRDDSLYGYEASDQSQA

Parental  TKLTILQSLGDPLYYGKIQPCKDDEESDSQTSPSHSSTDDHSNWFIIGSKTD
          TK...LQSL.DP...GK..PCK........T.P.HSSTDDH...F....KTD
Retrocopy TKQIFLQSLNDPFISGK-RPCKTSRCLRHMT-PHHSSTDDHLSSFLPWLKTD

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_401 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000116	2 retrocopies	retro_ecab_1052, retro_ecab_1101,
Homo sapiens	ENSG00000102710	2 retrocopies	retro_hsap_4659, retro_hsap_4794,
Loxodonta africana	ENSLAFG00000027507	1 retrocopy	retro_lafr_1199,
Macaca mulatta	ENSMMUG00000003590	2 retrocopies	retro_mmul_2479, retro_mmul_2555,
Pongo abelii	ENSPPYG00000005288	2 retrocopies	retro_pabe_3619, retro_pabe_3729,
Pan troglodytes	ENSPTRG00000005791	2 retrocopies	retro_ptro_3095, retro_ptro_3189,
Pteropus vampyrus	ENSPVAG00000014609	1 retrocopy	retro_pvam_401 ,
Tarsius syrichta	ENSTSYG00000013227	1 retrocopy	retro_tsyr_2160,
Vicugna pacos	ENSVPAG00000007288	1 retrocopy	retro_vpac_193,