RetrogeneDB ID: retro_amel_409

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192429.1:946139..946355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2S1
• Ensembl ID: ENSAMEG00000008394
• Aliases: None
• Description: adaptor-related protein complex 2, sigma 1 subunit [Source:HGNC Symbol;Acc:565]

Sequence

>retro_amel_409
TGCATCAACATGGACGTCAATGACAATAACCTGCCCTACCTGAAGATTTCCAGCTTTGTGGAAATCTTAAATGAGTGTTT
CCACAATGTCTGGGAGCTGGTGTTCAACTTCTACAAGGTTTACACAGTCGTGAATGAGATGTCCCCAGCTGGCGAGATCT
GAGAGACCAGCCAGATACTGGTGGTGACACAGCTGCTGAGGCTGCCATCTCTGCAG

Alignment

ORF - retro_amel_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.82 %
• Parental protein coverage: 54.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIREXIRETSQTKVLK
          CI..DVNDNNL.YL..I..FVE.LNE.FHNV.E..LVFNFYKVYTVV.EM..AGEI.E....TSQ..V..
Retrocopy CINMDVNDNNLPYLK-ISSFVEILNECFHNVWE--LVFNFYKVYTVVNEMSPAGEI*E----TSQILVVT

Parental  QLLMLQSLE
          QLL.L.SL.
Retrocopy QLLRLPSLQ

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_409 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_409 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002673	1 retrocopy	retro_amel_210,
Ailuropoda melanoleuca	ENSAMEG00000008394	1 retrocopy	retro_amel_409 ,
Macropus eugenii	ENSMEUG00000001062	2 retrocopies	retro_meug_1156, retro_meug_1993,
Mus musculus	ENSMUSG00000008036	1 retrocopy	retro_mmus_2739,
Rattus norvegicus	ENSRNOG00000015865	2 retrocopies	retro_rnor_1030, retro_rnor_1516,
Tursiops truncatus	ENSTTRG00000012548	1 retrocopy	retro_ttru_924,