RetrogeneDB ID: retro_amel_1777

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194276.1:63296..63601(+)
• Located in intron of: ENSAMEG00000008998

Retrocopy information

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

Parental gene information

• Parental gene symbol: C10ORF57
• Ensembl ID: ENSAMEG00000012986
• Aliases: None
• Description: None

Sequence

>retro_amel_1777
GTCACCGTCCTGGTGCTGGACTATTTCGTGTGGGTTGTCTTCTGGCCTCAGAGTATCCCTTGTCAGAGCATTGGGCCCTG
GGGCCTCTTCCCTCAGGACCTGGTGGACCATCATCACACCGTCCTACATGGTGGCCACTGGCTTGTGTGGTTAACTCACG
CCGGAGAGTCCTTGTAAACACGATTTTGTGCAAGTCTAAAGGCATCAGGGATGGTCGGGCTCAACTACTCTGGTTCCTAC
AAACTTTCCCCTTTGGGATAACATCTCTCTCCATCTCGATCGCTTACAGACCAAAAGGCCAAAAA

Alignment

ORF - retro_amel_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 80.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VITLSFGYYTWAVFWPQSIPYQSLGPLGLFTQYLVDHHHSLLHSGYWLAWLIHVGES-LYAMVLCKSKGI
          V..L...Y..W.VFWPQSIP.QS.GP.GLF.Q.LVDHHH..LH.G.WL.WL.H.GES.L....LCKSKGI
Retrocopy VTVLVLDYFVWVVFWPQSIPCQSIGPWGLFPQDLVDHHHTVLHGGHWLVWLTHAGES<LVNTILCKSKGI

Parental  TDGRAQLLWFLQTFLFGIASLSILIAYRPKRQK
          .DGRAQLLWFLQTF.FGI.SLSI.IAYRPK.QK
Retrocopy RDGRAQLLWFLQTFPFGITSLSISIAYRPKGQK

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_1777 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1777 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012986	4 retrocopies	retro_amel_1410, retro_amel_1554, retro_amel_1777 , retro_amel_821,
Bos taurus	ENSBTAG00000001656	1 retrocopy	retro_btau_316,
Homo sapiens	ENSG00000133678	1 retrocopy	retro_hsap_1692,
Mustela putorius furo	ENSMPUG00000003613	2 retrocopies	retro_mputfur_400, retro_mputfur_407,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Nomascus leucogenys	ENSNLEG00000010657	1 retrocopy	retro_nleu_1337,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Pongo abelii	ENSPPYG00000002293	1 retrocopy	retro_pabe_1393,