RetrogeneDB ID: retro_amel_804

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192649.1:1367353..1367864(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMRAL1
• Ensembl ID: ENSAMEG00000001876
• Aliases: None
• Description: NmrA-like family domain containing 1 [Source:HGNC Symbol;Acc:24987]

Sequence

>retro_amel_804
GCTGGGAGACGGGCAGTGGGCCACTTTGATGGCGAAGGGGAGGTGGAGGAATATTTCCGGGACCTTGGAGTTCCCATGAC
CTGCGTGTGGCTGTCCTGCTATTTCAAGAACCCCTTCTCCTTCTGCCCCAGAAAGTCCCTGATGGAACGAGCTCCTTGCT
GAGCTTGCCTATGAGGGATGTGCCTGTGGGTGGCCTATCTGTGACCCACTTGGGTCCTATGGTGCTTGGGCTGCTGAAGA
TGCCAGAAAAATACATGGGGCTCAGTACTTGCAGGCACCCATGCAAGAGGGTGCCGCCCTGCTCTCCAGGAGCAGCGGGA
AGGCTGTGAGCGATGCCAAGACCAGCCTGGAGGACCAGAAATACGGCTTCCCTGGAGTCTAGGGCCTGGCCAACATCACC
CCTTTCCCTGCCCTGAAAGCTGCAGGTGACATCAAACTGACCCTGAGGCTCAATCCCCAGGCCAGGATGCTGGACCTGTG
GCTGGAGTAGCACAGAGGCCACTGTGCTGGA

Alignment

ORF - retro_amel_804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.25 %
• Parental protein coverage: 59.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGRLAAGHFDGKGEVEEYFRDIGVPMTSVRLSCY-FENLLSYFLPQKAPDGKSYLLSLPMGDVPMDGLSV
          AGR.A.GHFDG.GEVEEYFRD.GVPMT.V.LSCY.F...L...LPQK.PDG.S.LLSLPM.DVP..GLSV
Retrocopy AGRRAVGHFDGEGEVEEYFRDLGVPMTCVWLSCY<FQEPL-LLLPQKVPDGTSSLLSLPMRDVPVGGLSV

Parental  TDLGPVVLSLLKMPEEYVGQNIGLSTCKHTA-EEYAALLSKHTGKTVRNAKTTPEDYEKYGFPGAQDLAN
          T.LGP.VL.LLKMPE.Y.G....LSTC.H....E.AALLS...GK.V..AKT..ED..KYGFPG...LAN
Retrocopy THLGPMVLGLLKMPEKYMG----LSTCRHPC<QEGAALLSRSSGKAVSDAKTSLED-QKYGFPGV*GLAN

Parental  MFRFYALKPDRDIELTLKLNPKARTLEQWLEQHKGDFAG
          ...F.ALK...DI.LTL.LNP.AR.L..WLE.H.G..AG
Retrocopy ITPFPALKAAGDIKLTLRLNPQARMLDLWLE*HRGHCAG

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_804 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_804 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001876	1 retrocopy	retro_amel_804 ,
Callithrix jacchus	ENSCJAG00000019832	1 retrocopy	retro_cjac_1067,