RetrogeneDB ID: retro_pvam_1009

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2232:161225..161559(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKLF
• Ensembl ID: ENSPVAG00000000188
• Aliases: None
• Description: chemokine-like factor [Source:HGNC Symbol;Acc:13253]

Sequence

>retro_pvam_1009
TTTATCATCTCACAGCCACTGAACCATATATCATATCACTGGATTTGAAATTATTGTTATTTTCTTTTTCATAATTATAT
ATATGCAAACTTGATCAATTAATGAAATGTTTATTTAGGCCTTTACTTGATATTATCAACTCACTGGTAACAACAACATT
CATGATAATCATATCTGTGTTCACACTGATACCAGAAACCATAATATTAACAGTCCTTAGAGGGGTTTTTGAACTTGTAG
AACAGTGTGCTGTATTGCTAGGCGGGCCTTTATTCACCAGAAGTTTCTATTTAATTCAAGCGGTTCTTATCAGGAGAGTG
CTATCCATGACAAA

Alignment

ORF - retro_pvam_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.12 %
• Parental protein coverage: 74.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FIISQ-APEPYIV-IAGFEVTVIFFFII-LYMFRLDRIINCIFWPLLDIINSVVTAIFMMTISVLALIPE
          FIISQ.A.EPYI..I.GFE..VIF.F.I.LY...LD....C.F.PLLDIINS.VT..FM..ISV..LIPE
Retrocopy FIISQ<ATEPYII<ITGFEIIVIF-FFI>LYICKLDQLMKCLFRPLLDIINSLVTTTFMIIISVFTLIPE

Parental  TTFM-ILGGAFGLLV-VVCSIADAALIYRKLLFNPSGPYRKSAIHDK
          T.....L.G.F.L....VC.IA..A.I..K.LFN.SG.Y..SAIHDK
Retrocopy TIILTVLRGVFELVE<TVCCIARRAFIHQKFLFNSSGSYQESAIHDK

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_1009 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000000188	1 retrocopy	retro_pvam_1009 ,
Sarcophilus harrisii	ENSSHAG00000000837	1 retrocopy	retro_shar_269,
Tarsius syrichta	ENSTSYG00000014768	1 retrocopy	retro_tsyr_671,