RetrogeneDB ID: retro_amel_678

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192564.1:891752..892309(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000015478
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HIBADH
• Ensembl ID: ENSAMEG00000005849
• Aliases: None
• Description: 3-hydroxyisobutyrate dehydrogenase [Source:HGNC Symbol;Acc:4907]

Sequence

>retro_amel_678
TATTCATGCATTATTTATGATCTGTTCTCTGATGCATACAAAGAGTTTCAAGATGTGAGTGAGCAGGTAGTGTATTCCTC
AGCAGATGTAGCTGAAAAAACTGACAGAATTATTACAATGTTGCTTACCAATATCAATGCAACAGAAGGTCATTCCGGAT
CAAATGAAATTCTAAAAAAAAGTGAAGAATGGCTCACTATTAATAGATTCCAGTACTATTGATCCTGCAATTTCAAAAGA
ATTGGCCAAAAAAATTGAGAAAATGGGAACAGTTCATGGATGCCCCTGTTTCTGGTGGTGTGGGAGCTGCTCCATCTGGG
AACCTCACATTTATGGTGGGAGGAGACGAAGATAAATTTGCTGCTGCCCAAGAGTTGCTGGGGTGCATGCGAGCCAGTGT
GGTGTATTGTGGAGCTGTAGGGACCAGGTTGACTGCAAAGATTTACAACATGCTATTAGCTACCAGAATGATTGGAACTG
CTGAAGCTATGAATCTTGGAATCAGGTTAGGGCATGACCCAAAGCTGTTGGCTAAAATCCTAAATTTGATCTCAGGA

Alignment

ORF - retro_amel_678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.13 %
• Parental protein coverage: 55.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YPLIIYDVFPDACKEFQDAGEQVVSSPADVAEKADRIITMLPTSINAIEAYSGANGILKK-VKKGSLLID
          Y..IIYD.F.DA.KEFQD..EQVV.S.ADVAEK.DRIITML.T.INA.E..SG.N.I....VK.GSLLID
Retrocopy YSCIIYDLFSDAYKEFQDVSEQVVYSSADVAEKTDRIITMLLTNINATEGHSGSNEIXXX>VKNGSLLID

Parental  SSTIDPAVSKELA-KEVEKMGAVFMDAPVSGGVGAARSGNLTFMVGGVEDEFAAAQELLGCMGSNVVYCG
          SSTIDPA.SKELA.K...K....FMDAPVSGGVGAA.SGNLTFMVGG.ED.FAAAQELLGCM...VVYCG
Retrocopy SSTIDPAISKELA>KKLRKWEQ-FMDAPVSGGVGAAPSGNLTFMVGGDEDKFAAAQELLGCMRASVVYCG

Parental  AVGTGQAAKICNNMLLAISMIGTAEAMNLGIRLGLDPKLLAKILNMSSG
          AVGT...AKI..NMLLA..MIGTAEAMNLGIRLG.DPKLLAKILN..SG
Retrocopy AVGTRLTAKI-YNMLLATRMIGTAEAMNLGIRLGHDPKLLAKILNLISG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_678 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_678 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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
Ailuropoda melanoleuca	ENSAMEG00000005849	1 retrocopy	retro_amel_678 ,
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997,
Microcebus murinus	ENSMICG00000000512	1 retrocopy	retro_mmur_1059,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792,