RetrogeneDB ID: retro_pvam_992

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_21309:7345..8015(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR1B
• Ensembl ID: ENSPVAG00000007116
• Aliases: None
• Description: ARP1 actin-related protein 1 homolog B, centractin beta (yeast) [Source:HGNC Symbol;Acc:168]

Sequence

>retro_pvam_992
GGGCTGCTGGCCCCGTGCCACCCCATGGAGCTCAACGTGGTATGGAACCGGAATGACATGTGGCAGTACGTCTACTCCAA
GGACCAGCCACAGCAGCCGCAGACCTTCTCCGAGGAGGATCCTGTGCTTCTAAAGGAAGCCCCGCTCAACCTGAGTAAGA
CCCGGGAGAAGGCAGCAGGGGGTTCTTTGAGACCCTCAACGTGCCAGCCCTGTTTATCCCCATGAAGTCCATGCTCAGCC
CGTATGCAAAGGAACGCACAACAGGAGTGGTTTTAGACTCGGCAGATGGGGTCATCCGTGCTGTCCCCACCTACGAGGGC
TTTGCCATGTCACGTTCCATCGCATAGGTGGACGTTGCCAGCTGTGATGTCTCCTGCTGACTCTGTTGCTGCTGCACCAG
GAAGACTTGACATTCACAGCTCAGCTGAGTTTGAGGTTGTCCAAACCATCAGAGAGAGAGCCTGCTGCCCCGTCCATCAA
CCTGCAGAAGGACGAGGCTCTGGAGACGGAGAAGATGCGGTATGCCCTGGCCAGATGACAGTACACTCCATGTGGGGCCA
GCGCGATTCAGGGCCCCAAGCTGCTGTTCCGGCAGGACCTGGTAAAGGACGGGAGCAAGGGGTTCCACAAGGTGCTGGCC
TTTGCCACCCACAAGTCCAACCTGGACCTC

Alignment

ORF - retro_pvam_992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.81 %
• Parental protein coverage: 59.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GLLALRHPMEHGVVRDWNDMERIWQYVYSKD---QLQTFSEEHPVLLTEAPLNPSKNREKAA-EVFFETF
          GLLA..HPME..VV...NDM...WQYVYSKD...Q.QTFSEE.PVLL.EAPLN.SK.REKAA...FFET.
Retrocopy GLLAPCHPMELNVVWNRNDM---WQYVYSKDQPQQPQTFSEEDPVLLKEAPLNLSKTREKAA<RGFFETL

Parental  NVPALFISMQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSIMRVDIAGRDVSRYL-RLLLRKE
          NVPALFI.M...LS.YA..RTTGVVLDS.DGV..AVP.YEGFAM..SI..VD.A..DVS..L..LLL..E
Retrocopy NVPALFIPMKSMLSPYAKERTTGVVLDSADGVIRAVPTYEGFAMSRSIA*VDVASCDVSC*L<LLLLHQE

Parental  G-VDFHTSAEFEVVRTIKERAC-YLSINPQKDEALETEKVQYTL-PDGSILDVGPARFRA-PELLFQPDL
          ...D.H.SAEFEVV.TI.ERAC...SIN.QKDEALETEK..Y.L.PD.S.L.VGPARFRA.P.LLF..DL
Retrocopy D<LDIHSSAEFEVVQTIRERAC>APSINLQKDEALETEKMRYAL>PDDSTLHVGPARFRA<PKLLFRQDL

Parental  VGDESEGLHEVLAFAIHKSDLDL
          V.D.S.G.H.VLAFA.HKS.LDL
Retrocopy VKDGSKGFHKVLAFATHKSNLDL

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_992 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	ENSPVAG00000007116	1 retrocopy	retro_pvam_992 ,
Tarsius syrichta	ENSTSYG00000000406	1 retrocopy	retro_tsyr_2031,
Drosophila melanogaster	FBgn0011745	1 retrocopy	retro_dmel_80,