RetrogeneDB ID: retro_amel_1533

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193567.1:30266..30625(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM162A
• Ensembl ID: ENSAMEG00000014316
• Aliases: None
• Description: family with sequence similarity 162, member A [Source:HGNC Symbol;Acc:17865]

Sequence

>retro_amel_1533
AGTTATTTTAGGTTATATGAAAGAGATGTCTCCTCATCTCTAAGACTTACCAGAAATCCTGATTTGAAGACAATAAGTGG
ATTTTGCACTAAACCACAAGTCAGTCTAAAAGCTCCATCCTACACTTCCAGCTGCAGAGCGCCATGACGCAAACTTACGT
GTTGGGAAATGAAGATCCTGATAGGTCAGGTCGCTTCAAAAAGGAAGATGAAATCCCAGAGACTGTCTTGTTTGAGATGC
TTGATGCTGCCAAGAACAAGATGTGGGGGAAGATAAGCTTTGTCATGATTGCCCTGACAGTGGCAGGATGCATCTCAATG
GTTGTTGAGGGCAAGAAGGCTGTCAAAAGAAATGAGTCT

Alignment

ORF - retro_amel_1533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.55 %
• Parental protein coverage: 75.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SYFRLYERGASSSLRLMRNSNLKRINGYCAKPQESPKAPPYTYSHRVPLHKPTHWERKILIW-SGRFKKE
          SYFRLYER..SSSLRL.RN..LK.I.G.C.KPQ.S.KAP.YT.S.R.P..K.T.WE.KILI..SGRFKKE
Retrocopy SYFRLYERDVSSSLRLTRNPDLKTISGFCTKPQVSLKAPSYTSSCRAP*RKLTCWEMKILIG<SGRFKKE

Parental  DEIPETVSFEMLDTAKNKIRVKVSYAMIALTVAGCIWMVIEGKKAVKRNES
          DEIPETV.FEMLD.AKNK...K.S..MIALTVAGCI.MV.EGKKAVKRNES
Retrocopy DEIPETVLFEMLDAAKNKMWGKISFVMIALTVAGCISMVVEGKKAVKRNES

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_1533 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1533 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014316	1 retrocopy	retro_amel_1533 ,
Monodelphis domestica	ENSMODG00000018300	1 retrocopy	retro_mdom_785,
Mustela putorius furo	ENSMPUG00000004773	1 retrocopy	retro_mputfur_1616,
Otolemur garnettii	ENSOGAG00000003194	1 retrocopy	retro_ogar_2064,
Rattus norvegicus	ENSRNOG00000002255	2 retrocopies	retro_rnor_2587, retro_rnor_337,
Tursiops truncatus	ENSTTRG00000013401	1 retrocopy	retro_ttru_791,