RetrogeneDB ID: retro_amel_436

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192441.1:2002591..2003073(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000010854
• Aliases: None
• Description: None

Sequence

>retro_amel_436
ATGGGGTGTTGTTACAGCAGCCAGAACAAGGACTTGAACTGGGACTGAGAGGAACAGAAGCTGCTGCTGGACCCTAATAG
CCCCCCTACCAAAGCCCTCAATGGAGCTGAGTCCAACTACCACAGTCTACCTCCCATTCATACAAATGAGTGGGCCCTGC
TTTCCTCCAGCCTTGCTAAGACAGCCAGCAACACCATTGGTGTGTCTGCTGCAGACTCCCAGGGCACGGAGCCCCATGAG
TATATGCATTAGGCAGGGCAGTACAGCATCCACTTGGCGGTGCTAAGCAGCAGTCTGACCACTGGAATAAGCTGCTGCCA
TTGCCATCTCTCACCAGCCAGCCCCACCAAGTGCTGGCCAGCAAGCCCATCCCCTTCTCTGACTTACAGCACGTCCCCAG
GATAGCTGCTTATGCCTACAGTGCACTTTCACAGATCTGAGTGGACACCAAAGAGGAGCTAGTTGTACAGTTTGGGATCC
CA

Alignment

ORF - retro_amel_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPPTRTDEQALLSSILAKTASNIIDVSA
          MGCCYSS.N.D...D.EE.KLLLDP.SPPTKALNGAE.NYHSLPP..T.E.ALLSS.LAKTASN.I.VSA
Retrocopy MGCCYSSQNKDLNWD*EEQKLLLDPNSPPTKALNGAESNYHSLPPIHTNEWALLSSSLAKTASNTIGVSA

Parental  ADSQGMEQHEYMDRARQYSTRLAVLSSSLT-HWKKLPPLPSLTSQPHQVLASEPVPFSDLQQVSRIAAYA
          ADSQG.E.HEYM..A.QYS..LAVLSSSLT.HW.KL.PLPSLTSQPHQVLAS.P.PFSDLQ.V.RIAAYA
Retrocopy ADSQGTEPHEYMH*AGQYSIHLAVLSSSLT<HWNKLLPLPSLTSQPHQVLASKPIPFSDLQHVPRIAAYA

Parental  YSALSQIRVDAKEELVVQFGIP
          YSALSQI.VD.KEELVVQFGIP
Retrocopy YSALSQI*VDTKEELVVQFGIP

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_436 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_436 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010854	2 retrocopies	retro_amel_1176, retro_amel_436 ,
Canis familiaris	ENSCAFG00000005788	1 retrocopy	retro_cfam_1962,
Echinops telfairi	ENSETEG00000010979	1 retrocopy	retro_etel_1005,
Felis catus	ENSFCAG00000005320	2 retrocopies	retro_fcat_142, retro_fcat_496,
Macropus eugenii	ENSMEUG00000003560	1 retrocopy	retro_meug_17,
Myotis lucifugus	ENSMLUG00000014117	1 retrocopy	retro_mluc_2372,
Mustela putorius furo	ENSMPUG00000010289	3 retrocopies	retro_mputfur_1178, retro_mputfur_270, retro_mputfur_455,
Mus musculus	ENSMUSG00000030842	2 retrocopies	retro_mmus_1805, retro_mmus_2538,
Rattus norvegicus	ENSRNOG00000020016	1 retrocopy	retro_rnor_2788,
Tarsius syrichta	ENSTSYG00000014730	2 retrocopies	retro_tsyr_1324, retro_tsyr_33,