RetrogeneDB ID: retro_amel_263

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192369.1:3848777..3849168(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM1
• Ensembl ID: ENSAMEG00000011141
• Aliases: None
• Description: LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:20472]

Sequence

>retro_amel_263
ATGAATGCTACGCCCAGCACCGCCAGCCTCATCGAGGACATCGACAAGAAGAACTTGGTCCTGATTCAAGATGGAAGGAC
GCTTACCGATTTTATAAGAAGCATTGATCAATTTGCTAATTTAGTGCTACATCAGACTGTGAAGCCTATTCACATGGGCA
AAAAATACAGTGATATACCTCAAGGGATTTTTGTGGTCGGAGGAGGAACTGTGGTCCTACTAGGAGAAATAGCTTAGAAA
GGAGAATGACACACCCCACCAGCAACTGCCCATTGAAATCCTAGAAGAACAAAGGGTAGAGGAGCAGACCAATTTGAAGG
CTGAGAAGCTGGAAGTTCAAGCTCTGGAGGATCGGGGTCTCTCCGTTCCTCAAGCAGAGACCGTTGACGAG

Alignment

ORF - retro_amel_263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.88 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNYMPGTASLIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGEN
          MN..P.TASLIEDIDKK.LVL..DGRTL..F.RSIDQFANLVLHQTV..IH.GKKY.DIP.GIFVV.G..
Retrocopy MNATPSTASLIEDIDKKNLVLIQDGRTLTDFIRSIDQFANLVLHQTVKPIHMGKKYSDIPQGIFVVGGGT

Parental  VVLLGEI-DLEK-ESDTPLQQVSIEEILEEQRVEQQTKLEAEKLKVQALKDRGLSIPRADTLDE
          VVLLGEI..LE..E.DTP.QQ..I.EILEEQRVE.QT.L.AEKL.VQAL.DRGLS.P.A.T.DE
Retrocopy VVLLGEI<SLER<ENDTPHQQLPI-EILEEQRVEEQTNLKAEKLEVQALEDRGLSVPQAETVDE

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_263 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_263 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011141	1 retrocopy	retro_amel_263 ,
Myotis lucifugus	ENSMLUG00000003734	1 retrocopy	retro_mluc_723,
Mustela putorius furo	ENSMPUG00000009883	1 retrocopy	retro_mputfur_490,
Mus musculus	ENSMUSG00000037296	1 retrocopy	retro_mmus_3725,
Oryctolagus cuniculus	ENSOCUG00000015399	1 retrocopy	retro_ocun_1276,
Sarcophilus harrisii	ENSSHAG00000017260	1 retrocopy	retro_shar_532,