RetrogeneDB ID: retro_pvam_523

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3595:255080..255503(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIDEB
• Ensembl ID: ENSPVAG00000007036
• Aliases: None
• Description: cell death-inducing DFFA-like effector b [Source:HGNC Symbol;Acc:1977]

Sequence

>retro_pvam_523
GGGATCTCAGTAGAAAGCAAAGACTTTTTCCAGCTGTTAAAAGATGACATATGCCTAATGGTGCAGGAGTCGGGACACAG
CTGGAGCCCCAGCAGGAGTGGGTGTTGTCTTACAGCCTAGGCTGGGAGAAGCCCAAGCACAGCAAAGACATCACCCTCAT
CACCTTCAACACATATGAGCAAAACCCTCGAGACCTCTTTTGCAACCTGAATGTCAAAGCCACATTCTACGGGCTCTACT
CCATGAGTTGTGACTTTTGAGGACCTGGACCCAAAAATGTACTCAAGGACCTCCTGCAATTGGACTTCTATACTGCTGCA
AGACTTGCGCCATATATCATCGGGAATTTCCTCCACCCTTCACCATGCAGAAGAGCAGGCTGAGCAGTGGCTGTGGCAGC
AGCAGGATTGCCTCTCTCCCTAC

Alignment

ORF - retro_pvam_523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.83 %
• Parental protein coverage: 63.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GTAVESEDFFQLLEDDTCLMVLESGQSWSPSRSG-VLLYGLGREKPKYSKDIARITFDMYKQNPRDLFGS
          G..VES.DFFQLL.DD.CLMV.ESG.SWSPSRSG.VL.Y.LG.EKPK.SKDI..ITF..Y.QNPRDLF..
Retrocopy GISVESKDFFQLLKDDICLMVQESGHSWSPSRSG<VLSYSLGWEKPKHSKDITLITFNTYEQNPRDLFCN

Parental  LNIQATFYGLYSMSCDIQGLGPKKVLRELLR-WTSTLLQGLGHMLLGISSTLRHVVEGAGQW---QQGRL
          LN..ATFYGLYSMSCD..G.GPK.VL..LL..WTS.LLQ.L.H...GISSTL.H..E.A.QW...QQ..L
Retrocopy LNVKATFYGLYSMSCDF*GPGPKNVLKDLLQ>WTSILLQDLRHISSGISSTLHHAEEQAEQWLWQQQDCL

Parental  HPY
          .PY
Retrocopy SPY

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_523 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016089	1 retrocopy	retro_amel_633,
Canis familiaris	ENSCAFG00000012240	1 retrocopy	retro_cfam_85,
Equus caballus	ENSECAG00000010495	1 retrocopy	retro_ecab_943,
Felis catus	ENSFCAG00000026821	1 retrocopy	retro_fcat_1418,
Pteropus vampyrus	ENSPVAG00000007036	1 retrocopy	retro_pvam_523 ,