RetrogeneDB ID: retro_pvam_96

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1334:64185..64651(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRAM2
• Ensembl ID: ENSPVAG00000005429
• Aliases: None
• Description: DNA-damage regulated autophagy modulator 2 [Source:HGNC Symbol;Acc:28769]

Sequence

>retro_pvam_96
GTTTTATGCACTGCTACCATTTATGTTTGTTATAAGCAAGTTCATGCTCTCAATCCTGAAGGGAGTTGTATCACCAGATT
AAACAAGGATGGCCTTGTACTTGGATTGCTGAGTGGTTTATAACATTCTACTGTGGCAAACTTCCAGAAAATAATCTTTG
TTATTGTACATGTATGTGGAGTTGTGCTCACCTTTGGTGTGGGCTCATCATACATGTTTGTTTAGACCATCCTTTCCTAC
CAGACTCAGCCCAAAATGCATGGGACACGAATCCTCTGGATCAGACTTCTGGTGGTTATCTGGAGTGGAGTAAGTGCACT
TAGCATTGCTGACTCACTCATCACTTTTGCACAGTGGCAGTTTTGGCACAGATGTAGTACAGAAACTCCACTGGAACCCT
GAGAACAAAGGTTATGGGCTTCGCATAATCACTACTGCAGCAGAATGGTCTAGGTCGTCTTCCTTC

Alignment

ORF - retro_pvam_96 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 58.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLCVATIYVRYKQVHALNPERNCIIRLNKAGLVLGLLSCLGLSLVANFQKTTFFVVHVCGAVLTFGMGSL
          VLC.ATIYV.YKQVHALNPE..CI.RLNK.GLVLGLLS.L..S.VANFQK..F..VHVCG.VLTFG.GS.
Retrocopy VLCTATIYVCYKQVHALNPEGSCITRLNKDGLVLGLLSGL*HSTVANFQKIIFVIVHVCGVVLTFGVGSS

Parental  YMFVQTILSYQMQPKIHGKQVFWIRLLVVIWCGVSAFS-MLTCSSLLYSGSFGTDIVQKLHWNPKDKGYV
          YMFV.TILSYQ.QPK.HG....WIRLLVVIW.GVSA.S..LT.SSLL.SGSFGTD.VQKLHWNP..KGY.
Retrocopy YMFV*TILSYQTQPKMHGTRILWIRLLVVIWSGVSALS>LLTHSSLLHSGSFGTDVVQKLHWNPENKGYG

Parental  LHMITTAAEWSMSFSF
          L..ITTAAEWS.S.SF
Retrocopy LRIITTAAEWSRSSSF

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_96 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017009	1 retrocopy	retro_dnov_2336,
Loxodonta africana	ENSLAFG00000007736	1 retrocopy	retro_lafr_688,
Myotis lucifugus	ENSMLUG00000005097	1 retrocopy	retro_mluc_372,
Mustela putorius furo	ENSMPUG00000004232	1 retrocopy	retro_mputfur_446,
Pteropus vampyrus	ENSPVAG00000005429	2 retrocopies	retro_pvam_1424, retro_pvam_96 ,