RetrogeneDB ID: retro_pvam_1157

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_33464:3427..4080(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000013502
• Aliases: None
• Description: None

Sequence

>retro_pvam_1157
AGAGCTTTTAAACTAACAAGAGATGCTATTGAGTTAAATGCAGCCAATTACACAGTGTGGTATTTTTGAAAAGTTCTCTT
AAAGACATTTCAAAGGAATCTACATGAGAAAATGTACTACATCACTGCAATAACTGAACAGCCCAAAAACTATCGAGTTT
GGCATCACGGGCATTAGTGAAATGGCTAAAAAATCCATCTTAGGAGCTTGAGTTTGTTGCTGATATTCTTAATCAGGATG
CAAAGAATTATCACACCTAGCAACATCGACAGTGAGTTATTCAGGAATTTAAACTCTGGGGTAATGAGTTGCAGTATGTA
GACCAACTTCTTAAAGAGGATGTGAGAAATAACTCTGGAAGATACTTCGTCATTTTTAACACCACTGGCTACAATAATCA
TGCTATATTGGAGAGAGAAGTCCAGATCACTCTGGAAATGATCAAATTAGTACCATATAATGAAAGTGCCTGGACCTATT
TGAAAGAGATTTTGCAGAATCATGGTCTTTCCAAACATCCCAATCTGTTAAATCAATTACTTGATTTACAACCAAGTCAC
AGTTTCCCCTACCTAACTGCCTTTCTCATGGATATCTATGAAGATATGCTAGAAAACCAATGCGGTGACAAGAAGGACAC
TCTTCATGAAGCA

Alignment

ORF - retro_pvam_1157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.02 %
• Parental protein coverage: 59.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHR-RVLVEWLKDPS
          RAFKLTRDAIELNAANYTVW.F..VLLK..Q..LHE.M.YITAI.E.QPKNY.VW.H..R.LV.WLK.PS
Retrocopy RAFKLTRDAIELNAANYTVWYF*KVLLKTFQRNLHEKMYYITAITE-QPKNYRVW-HH<RALVKWLKNPS

Parental  QELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDR
          .ELEF.ADILNQDAKNYH..QHRQ.VIQEFKLW.NELQYVDQLLKEDVRNNS....RYFVI.NTTGYN..
Retrocopy *ELEFVADILNQDAKNYHT*QHRQ*VIQEFKLWGNELQYVDQLLKEDVRNNS---GRYFVIFNTTGYNNH

Parental  AILEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDML
          AILEREVQ.TLEMIKLVP.NESAW.YLK.ILQ..GLSK.PNLLNQLLDLQPSHS.PYL.AFL.DIYEDML
Retrocopy AILEREVQITLEMIKLVPYNESAWTYLKEILQNHGLSKHPNLLNQLLDLQPSHSFPYLTAFLMDIYEDML

Parental  ENQCDNKEDILNKA
          ENQC..K.D.L..A
Retrocopy ENQCGDKKDTLHEA

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_1157 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003201	2 retrocopies	retro_btau_1431, retro_btau_1768,
Canis familiaris	ENSCAFG00000005385	1 retrocopy	retro_cfam_941,
Homo sapiens	ENSG00000168522	1 retrocopy	retro_hsap_805,
Macaca mulatta	ENSMMUG00000017158	1 retrocopy	retro_mmul_1078,
Monodelphis domestica	ENSMODG00000010003	1 retrocopy	retro_mdom_1656,
Nomascus leucogenys	ENSNLEG00000012979	1 retrocopy	retro_nleu_2408,
Pteropus vampyrus	ENSPVAG00000013502	2 retrocopies	retro_pvam_1157 , retro_pvam_1433,
Tursiops truncatus	ENSTTRG00000008870	1 retrocopy	retro_ttru_579,