RetrogeneDB ID: retro_amel_210

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192353.1:1271156..1271457(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S1
• Ensembl ID: ENSAMEG00000002673
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 1 subunit [Source:HGNC Symbol;Acc:559]

Sequence

>retro_amel_210
AGGCCCATGATGTGCAGCTTCCTGCGGTAGAAGGACCTCAAAGTCGTCTATAAAAGATACGCCGTCTCTACTTCAGCGGC
GCCATGGAGCGCCTGGACAATGAACTCCTAACGCTGGAGCTGAGCCACCGAGGTGTGAAGCTCCTGGACAATACTGCCGC
AGCGTGTGCGAGATGGCCTTCCTCTTTAACTTTGAGAAGGCCTGCTTCCTCTAGTATGACGTTTCGAGGAGGAGTGATGT
CCAGGACAGCTTCAGGAAGGCCGTGACGCAGGCTGACGCGCTGCAGGAGGAGGGGCGCTCT

Alignment

ORF - retro_amel_210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.01 %
• Parental protein coverage: 55.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPKMCSFLEWRDLKVVYKRYA-SLYFCCAIEGQDNELITLELIHRYVELLD-KYFGSVCELDIIFNFEKA
          .P.MCSFL...DLKVVYKRYA..LYF..A.E..DNEL.TLEL.HR.V.LLD..Y..SVCE....FNFEKA
Retrocopy RPMMCSFLR*KDLKVVYKRYA<RLYFSGAMERLDNELLTLELSHRGVKLLD<QYCRSVCEMAFLFNFEKA

Parental  YFILDEFLMGGDVQDTSKKSVLKAIEQADLLQEEDES
          .F.........DVQD...K....A..QAD.LQEE..S
Retrocopy CFL*YDVSRRSDVQDSFRK----AVTQADALQEEGRS

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_210 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_210 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002673	1 retrocopy	retro_amel_210 ,
Ailuropoda melanoleuca	ENSAMEG00000008394	1 retrocopy	retro_amel_409,
Felis catus	ENSFCAG00000029169	1 retrocopy	retro_fcat_152,
Homo sapiens	ENSG00000106367	1 retrocopy	retro_hsap_3765,
Macropus eugenii	ENSMEUG00000016245	3 retrocopies	retro_meug_1011, retro_meug_154, retro_meug_2051,
Microcebus murinus	ENSMICG00000005406	2 retrocopies	retro_mmur_1026, retro_mmur_1368,
Myotis lucifugus	ENSMLUG00000009898	2 retrocopies	retro_mluc_1493, retro_mluc_2061,
Mustela putorius furo	ENSMPUG00000015867	1 retrocopy	retro_mputfur_1184,
Pan troglodytes	ENSPTRG00000019520	3 retrocopies	retro_ptro_1234, retro_ptro_24, retro_ptro_2554,