RetrogeneDB ID: retro_amel_1062

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192876.1:117583..117950(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2orf76
• Ensembl ID: ENSAMEG00000008507
• Aliases: None
• Description: chromosome 2 open reading frame 76 [Source:HGNC Symbol;Acc:27017]

Sequence

>retro_amel_1062
AAGACAACTCCCATCATAGGTCACCTCATTCGTTCATTTGAGCATTATAATTTCAAACCTGTAGGATATCACAGAGTTAA
TTTGGACCAAACTACATAGGAGTTTATAGTATTTCTAAAGCAAGATGAGCCCTTAAGGACCAGCCTCTCACCGCCATTTG
GGAATTACAAATGTGATAAACAAAAGATTATTCACCAAGCTTATAGACCAAAGACAAGTGAACTTGTGTTGAGTTTGGGA
GATGACAGAGTCCCATCTAAAAGAAGACAGGACTCCAAAATCAGCTAGAATGGCCAATGAAGCTGAAATTGCATTCTTTT
GTGAAGAAGATTAGAACAACTACAAAACTAATCCCATTTAATCCTGG

Alignment

ORF - retro_amel_1062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.94 %
• Parental protein coverage: 97.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGVTITVRLIRSFEHRNFRPVVYHGVNLDQTTKEFILFLKQDIPLRTSLPPPFRNYKYDKLKIVHQAHRA
          K...I...LIRSFEH.NF.PV.YH.VNLDQTT.EFI.FLKQD.PLRTSL.PPF.NYK.DK.KI.HQA.R.
Retrocopy KTTPIIGHLIRSFEHYNFKPVGYHRVNLDQTT*EFIVFLKQDEPLRTSLSPPFGNYKCDKQKIIHQAYRP

Parental  KSNELVLSLEDDDTLM-LEEDSTLRTAGIAHETEIAFFCEEDYKNYKANPISSW
          K..ELVLSL..DD....L.ED.T...A..A.E.EIAFFCEED..NYK.NPI.SW
Retrocopy KTSELVLSL-GDDRVP>LKEDRTPKSARMANEAEIAFFCEED*NNYKTNPI*SW

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_1062 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1062 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008507	2 retrocopies	retro_amel_1062 , retro_amel_1693,
Bos taurus	ENSBTAG00000010599	1 retrocopy	retro_btau_965,
Canis familiaris	ENSCAFG00000004896	2 retrocopies	retro_cfam_1119, retro_cfam_1727,
Equus caballus	ENSECAG00000002063	1 retrocopy	retro_ecab_384,
Myotis lucifugus	ENSMLUG00000004031	1 retrocopy	retro_mluc_1204,
Mustela putorius furo	ENSMPUG00000000943	1 retrocopy	retro_mputfur_726,
Mus musculus	ENSMUSG00000026388	1 retrocopy	retro_mmus_947,
Pteropus vampyrus	ENSPVAG00000011615	1 retrocopy	retro_pvam_337,
Sus scrofa	ENSSSCG00000015718	1 retrocopy	retro_sscr_311,