RetrogeneDB ID: retro_amel_1604

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193715.1:286103..286407(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AAMDC
• Ensembl ID: ENSAMEG00000002128
• Aliases: None
• Description: adipogenesis associated, Mth938 domain containing [Source:HGNC Symbol;Acc:30205]

Sequence

>retro_amel_1604
ATGCCCTCCCCTAAAATTGCTTCCCTGTATGGGGGCAAATGAAAGTACAAGGCTCTACAAAAACCTATAAGTACTGCAAA
GTGTGGCCAGGGGAAGTCGGGCTTGGGATTGGAGAGATATAGGAACTGAGCATTCTCCTTATATGCAGCCTGCAGATGTG
GAGGAAGTTGTCAAGAAGGGCATGCAGACCCTTTTGATTGGCTGAGGGATGAGTGAGGCCTTGAAGGTGCCTCCAACAAC
TGCAAAGTGCCTGGAGAAACAAGGCATTAATGTGCGGGTCCTGCAGACAGAGCAGGGATTCAAG

Alignment

ORF - retro_amel_1604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 83.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSPEIA-FLSWGQMKVQGSAKTYKDCKVWPG-GSRAWDWRETGTEHSPGVQPADVEEVVKKGVQTLVIG
          M.SP.IA.F..WGQMKVQGS.KTYK.CKVWPG.GSRAWDWR..GTEHSP..QPADVEEVVKKG.QTL.IG
Retrocopy MPSPKIA<FPVWGQMKVQGSTKTYKYCKVWPG<GSRAWDWRDIGTEHSPYMQPADVEEVVKKGMQTLLIG

Parental  RGMSEALKVPPSTVEYLEKQGIDVRVLQTEQAVK
          .GMSEALKVPP.T...LEKQGI.VRVLQTEQ..K
Retrocopy *GMSEALKVPPTTAKCLEKQGINVRVLQTEQGFK

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_1604 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1604 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002128	1 retrocopy	retro_amel_1604 ,
Callithrix jacchus	ENSCJAG00000014890	1 retrocopy	retro_cjac_165,
Echinops telfairi	ENSETEG00000006423	1 retrocopy	retro_etel_187,
Felis catus	ENSFCAG00000007450	1 retrocopy	retro_fcat_8,
Loxodonta africana	ENSLAFG00000000518	1 retrocopy	retro_lafr_784,
Microcebus murinus	ENSMICG00000000300	2 retrocopies	retro_mmur_157, retro_mmur_424,
Mustela putorius furo	ENSMPUG00000015932	1 retrocopy	retro_mputfur_1468,
Rattus norvegicus	ENSRNOG00000012584	1 retrocopy	retro_rnor_2097,
Tarsius syrichta	ENSTSYG00000002262	1 retrocopy	retro_tsyr_1886,
Tursiops truncatus	ENSTTRG00000007111	1 retrocopy	retro_ttru_406,