RetrogeneDB ID: retro_amel_1340

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193218.1:626580..626844(-)
• Located in intron of: ENSAMEG00000015394

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96B
• Ensembl ID: ENSAMEG00000017164
• Aliases: None
• Description: family with sequence similarity 96, member B [Source:HGNC Symbol;Acc:24261]

Sequence

>retro_amel_1340
GGAGAACTGGACACCGGTCCCCTCCTTGTCTGTGAGCACTCTGGGGGACACCTGGTGACTGTGGACGAAGAGGACAAGCA
GGTTCCCAGTAGCAGTGGTGTGCACAGAGCCTTTGATCCCATTTGCTCCATCAGTGTCCCCGAGCTGCCACAGCCCCTAG
AAGAATGGAATGTTGTAGAGCAAGTCCAGGTTCAGGTGAACCACCCTGAGAACATGGCGGCCGTGGCCTTCGTACCCATG
CTCCCGCACCACAGCACGGCCACC

Alignment

ORF - retro_amel_1340 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.22 %
• Parental protein coverage: 54.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLLENANPLIYERSGERPVTAGEEDEQVPDSIDAREIFFPHLIRSINDPEHPLTLEELNVVEQVRVQVSD
          G.L.....L..E.SG...VT..EED.QVP.S......F.P..I.SI..PE.P..LEE.NVVEQV.VQV..
Retrocopy GELDTGPLLVCEHSGGHLVTVDEEDKQVPSSSGVHRAFDP--ICSISVPELPQPLEEWNVVEQVQVQVNH

Parental  PESTVAVAFTPTIPHCSMAT
          PE...AVAF.P..PH.S.AT
Retrocopy PENMAAVAFVPMLPHHSTAT

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_1340 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1340 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	ENSAMEG00000002448	1 retrocopy	retro_amel_1707,
Ailuropoda melanoleuca	ENSAMEG00000017164	1 retrocopy	retro_amel_1340 ,
Bos taurus	ENSBTAG00000013931	1 retrocopy	retro_btau_609,
Canis familiaris	ENSCAFG00000020394	2 retrocopies	retro_cfam_479, retro_cfam_802,
Felis catus	ENSFCAG00000029216	2 retrocopies	retro_fcat_1464, retro_fcat_697,
Mustela putorius furo	ENSMPUG00000005303	2 retrocopies	retro_mputfur_1547, retro_mputfur_302,
Mus musculus	ENSMUSG00000031879	1 retrocopy	retro_mmus_2927,
Sarcophilus harrisii	ENSSHAG00000004698	1 retrocopy	retro_shar_590,
Tarsius syrichta	ENSTSYG00000005006	2 retrocopies	retro_tsyr_1305, retro_tsyr_149,