RetrogeneDB ID: retro_pvam_93

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1328:143266..143707(+)
• Located in intron of: ENSPVAG00000000400

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL27A
• Ensembl ID: ENSPVAG00000002887
• Aliases: None
• Description: ribosomal protein L27a [Source:HGNC Symbol;Acc:10329]

Sequence

>retro_pvam_93
CCATCCAGACTGAGGAAGACCTGGAAACTTCGGGGCCACATAACCCATGCCCATGGCCACATCGGCAAGCACTGGAAGCA
CACAAGAAGCCAAAGTAATGCTGGTGACACGCATCACCACAACATCAACTTCAACAAATAACACCCAAATTACTTTGGGA
AAGTTAGTATGAAGTATTTCCACTTAAAGAGGAACCAGAGCTTCTGCTCATCTGTCAACCTTGATAAACTTGGACCTCGG
TCAATAAGCAGACATGAGTGAGTGCTGCCAAATACAAGAGCGGAGCTGCTCCTATCATTGACGAGGTATGATCAGGCTAC
TACAAAGTTCTGGGGATGAGAAAGCTCCCAAAGCAGCCTGTCATCATGAAGGTCAAATTCTTCAACAGACGAGCTGAAGA
GAAGATTAAGGGTGTTGCGGGAGGACTGTGTCTTGGTAGCT

Alignment

ORF - retro_pvam_93 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.48 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFCP
          PSRLRKT.KLRGH..H.HG.IGKH.KH.....NAG..HHH.INF.K.HP.YFGKV.M...HLKRNQSFC.
Retrocopy PSRLRKTWKLRGHITHAHGHIGKHWKHTRSQSNAGDTHHHNINFNK*HPNYFGKVSMKYFHLKRNQSFCS

Parental  TVNLDKL-WTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGV
          .VNLDKL.WT.V..QT.V.AAK.K.GAAPIID.V.SGYYKVLG..KLPKQPVI.K.KFF.RRAEEKIKGV
Retrocopy SVNLDKL<WTSVNKQT*VSAAKYKSGAAPIIDEV*SGYYKVLGMRKLPKQPVIMKVKFFNRRAEEKIKGV

Parental  GGA-CVLVA
          .G..CVLVA
Retrocopy AGG>CVLVA

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_93 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 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004205	15 retrocopies	retro_amel_1095, retro_amel_1160, retro_amel_1165, retro_amel_130, retro_amel_1311, retro_amel_1441, retro_amel_1673, retro_amel_393, retro_amel_450, retro_amel_497, retro_amel_521, retro_amel_693, retro_amel_752, retro_amel_966, retro_amel_989,
Bos taurus	ENSBTAG00000005349	2 retrocopies	retro_btau_126, retro_btau_45,
Canis familiaris	ENSCAFG00000006936	2 retrocopies	retro_cfam_145, retro_cfam_384,
Callithrix jacchus	ENSCJAG00000011775	1 retrocopy	retro_cjac_211,
Microcebus murinus	ENSMICG00000002296	4 retrocopies	retro_mmur_1309, retro_mmur_459, retro_mmur_612, retro_mmur_835,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Oryctolagus cuniculus	ENSOCUG00000005442	1 retrocopy	retro_ocun_12,
Pteropus vampyrus	ENSPVAG00000002887	14 retrocopies	retro_pvam_1087, retro_pvam_1130, retro_pvam_1135, retro_pvam_119, retro_pvam_1305, retro_pvam_198, retro_pvam_392, retro_pvam_54, retro_pvam_546, retro_pvam_575, retro_pvam_837, retro_pvam_84, retro_pvam_93 , retro_pvam_993,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,