RetrogeneDB ID: retro_pvam_1165

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3509:14898..15372(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDHD1
• Ensembl ID: ENSPVAG00000011149
• Aliases: None
• Description: haloacid dehalogenase-like hydrolase domain containing 1 [Source:HGNC Symbol;Acc:16818]

Sequence

>retro_pvam_1165
CCTGCTACTCACCCACTCTTTTACATGAATGGCCTCCTTCTGGACACTGAATGGCTCTATTCAGTGGAGTTTTAAGAAAT
ATGCGATCACTATGAGAAGCAATACACCTGGCATGTAAAGTCCCTCGTTATGGACACAAAGGGATTAGAGGTGGCTCTGA
TCGTAATAGATACCCTGCAGTTTCCCATGTCCAAAGAAGAGCTGGTGGAAGAAAGCCAGATGAAGCCAAAAGAAGTGTTG
CCCACGGCTGCTCTGATGCCAGCACTGGAAAAACTGATCCACCATCAGCAAAAGCACCACGTGCCCTTGGCTGTGGTCAT
CAGCTCTGAGTTTATATCCTTCGAGATGAAGACCAATGGACACAAGAAATTCTTCAGCTGGTTTGATTACATCGTTTTGG
TGGATGACCCCGAACTGAGGAACGGCAAGCCCGATCCAGACATATTTCTTGCTTGTGCAAAGGGGCTTTCCCCT

Alignment

ORF - retro_pvam_1165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.39 %
• Parental protein coverage: 68.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVTHLLFDLDGLLLDTERLYSVVFQEICGRYGKTYSWDVKSLVMGKKAFEAAQVIIDVLQLPMSKEELVA
          P.TH.LF...GLLLDTE.LYSV.F.EIC..Y.K.Y.W.VKSLVM..K..E.A...ID.LQ.PMSKEELV.
Retrocopy PATHPLFYMNGLLLDTEWLYSVEF*EICDHYEKQYTWHVKSLVMDTKGLEVALIVIDTLQFPMSKEELVE

Parental  ESQARLEALFPTAGLLPGVEKLIHHLRKHRVPFAVATSSGSDTFVMKTSAHKAFFSLFHHVVLGDDPEVK
          ESQ.......PTA.L.P..EKLIHH..KH.VP.AV..SS....F.MKT..HK.FFS.F...VL.DDPE..
Retrocopy ESQMKPKEVLPTAALMPALEKLIHHQQKHHVPLAVVISSEFISFEMKTNGHKKFFSWFDYIVLVDDPELR

Parental  NGKPDPDIFLACARRFLP
          NGKPDPDIFLACA....P
Retrocopy NGKPDPDIFLACAKGLSP

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_1165 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004616	1 retrocopy	retro_acar_48,
Choloepus hoffmanni	ENSCHOG00000001318	5 retrocopies	retro_chof_1597, retro_chof_1855, retro_chof_1883, retro_chof_2136, retro_chof_2168,
Homo sapiens	ENSG00000130021	2 retrocopies	retro_hsap_2469, retro_hsap_454,
Gorilla gorilla	ENSGGOG00000004425	1 retrocopy	retro_ggor_1537,
Microcebus murinus	ENSMICG00000017082	1 retrocopy	retro_mmur_1321,
Macaca mulatta	ENSMMUG00000017377	1 retrocopy	retro_mmul_244,
Monodelphis domestica	ENSMODG00000017505	2 retrocopies	retro_mdom_1374, retro_mdom_52,
Pongo abelii	ENSPPYG00000020105	2 retrocopies	retro_pabe_1837, retro_pabe_280,
Pteropus vampyrus	ENSPVAG00000011149	1 retrocopy	retro_pvam_1165 ,
Tarsius syrichta	ENSTSYG00000013238	4 retrocopies	retro_tsyr_2013, retro_tsyr_345, retro_tsyr_542, retro_tsyr_931,