RetrogeneDB ID: retro_pvam_371

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2775:61442..62203(+)
• Located in intron of: ENSPVAG00000001289

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3F
• Ensembl ID: ENSPVAG00000015764
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit F [Source:HGNC Symbol;Acc:3275]

Sequence

>retro_pvam_371
CCCCCAGCAGCCATAGTCCAGTTGCACCAAGTCACTTTGGCCTCCATCATGAATGGCTATGAGAGATGCAACAAAGGTGC
AGCCCAAGTTATCAGGACCCTGCTGGGAACTGCTGACAAGCACAGAGTGGAAGTCACCAATTGCTTTTCAGTGCCAATGA
GTCAGAAGAAGAGGTTGCTGTTGACATGGAATTTGCTAAGAACATGTATGAATTGCTCAGGAAAGTCCCTCCCAAATGAG
CTCATCCTGAGCTGATATGCTACAGGCCATGATATCACAGAGCAGTCTGTGCTGATCCATGAGTACTACAGCTGGGAAGC
CCCAAACCCATTCACCTCATGGTGGACTGGAGCCTCTGGAACAGCCGCATGAACATCAAGACCTATGTCAGCACTTTAAT
GGGTATCCCTGGGAGGACCATGGGAGTGATGTTCCCACCTCTGACCATGAAATATGCATTTTTGGACACTGAATGCATTG
GAGTTGACCTGATCCATGAAGACCTGCTTTAGCCCCAACTGGATAATTGGACTCTCAAGTGACTTGCAGCAAGTAGCAGA
GTCATTGGCTCGCATCCCGGATGCCCGAAGCACAGTGTTGCAGTATGTGGAAGACATACTGTCTGGAAAGGTGTCAGCTG
ACAAACTGTAGGCTGCTTCTTGACTAGTCTAGTTAACCGAGTATCCAAGCCAGTTCCTGATGACATCAAGACCATGCTCA
ACAGCAGCATCAATGACCTGCTGATGATGACCTACCTGGCA

Alignment

ORF - retro_pvam_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.77 %
• Parental protein coverage: 71.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTNCFSVPHNESEDEVAVDMEFAKNM
          P....V.LH.V.LASI...YER.N.GAA.VI.TLLGT.DKH.VEVTNCFSVP..................
Retrocopy PPAAIVQLHQVTLASIMNGYERCNKGAAQVIRTLLGTADKHRVEVTNCFSVPMSQKK-RLLLTWNLLRTC

Parental  YELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPN-PIHLTVDTSLQNGRMSIKAYVSTLMGVPG
          .....K..PNELIL..YATGHDITE.SVLIHEYYS.EAPN.PIHL.VD.SL.N.RM.IK.YVSTLMG.PG
Retrocopy MNCSGKSLPNELILS*YATGHDITEQSVLIHEYYSWEAPN<PIHLMVDWSLWNSRMNIKTYVSTLMGIPG

Parental  RTMGVMFTPLTVKYAYYDTERIGVDLI-MKTCFSPNRVIGLSSDLQQVAGSSARIQDALSTVLQYAEDVL
          RTMGVMF.PLT.KYA..DTE.IGVDLI.MKTCFSPN..IGLSSDLQQVA.S.ARI.DA.STVLQY.ED.L
Retrocopy RTMGVMFPPLTMKYAFLDTECIGVDLI>MKTCFSPNWIIGLSSDLQQVAESLARIPDARSTVLQYVEDIL

Parental  SGKVSAD-NTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLA
          SGKVSAD..TVG.FL.SLVN.V.K.VPDD..TMLNS.INDLLM.TYLA
Retrocopy SGKVSAD<QTVGCFLTSLVNRVSKPVPDDIKTMLNSSINDLLMMTYLA

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_371 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Gorilla gorilla	ENSGGOG00000011702	5 retrocopies	retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589, retro_ggor_1590,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Oryctolagus cuniculus	ENSOCUG00000004225	1 retrocopy	retro_ocun_1488,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175,
Pteropus vampyrus	ENSPVAG00000005186	1 retrocopy	retro_pvam_690,
Pteropus vampyrus	ENSPVAG00000015764	1 retrocopy	retro_pvam_371 ,