RetrogeneDB ID: retro_amel_346

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192394.1:393520..393841(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMIM19
• Ensembl ID: ENSAMEG00000005067
• Aliases: None
• Description: small integral membrane protein 19 [Source:HGNC Symbol;Acc:25166]

Sequence

>retro_amel_346
CTGCCTGGAGTTTAGGGGGTGATGGGTACCAATGGCTCTATTAATTATGGCCTTAAAAAGGCTTAGAATGAAGCCACCAA
CTTTTGCTGGGTTGGGATCCTTGACAGCTTTGGGCTCCTCATGTGTATCAAAAGGAATAAAAAGAAAATTATGAGGGTAT
TCAGTGTGCCACCTACAGCAGTAACTTCATCAGAGCCCAACTTTCATGACGCAATAAGCAAAATTCATTTAAGATAGCAA
TTGGAAATGAATTCCATTTCCAGGAAGTCTGACTACCAGCAGCCATAAAACCAAGCTAACAATATGCGGCTCTTATTGGA
A

Alignment

ORF - retro_amel_346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGAYGVMGDDGSMDYSVHEAWNEATNVYLVVILVSFVLFVYAKRNKRKIMRIFSVPPTAETLSEPSFYD
          .PG..GVMG..GS..Y....A.NEATN...V.IL.SF.L....KRNK.KIMR.FSVPPTA.T.SEP.F.D
Retrocopy LPGV*GVMGTNGSINYGLKKA*NEATNFCWVGILDSFGLLMCIKRNKKKIMRVFSVPPTAVTSSEPNFHD

Parental  TISKIRLRQQLEMYSISRKYDYQQPQNQADSVQLSLE
          .ISKI.LR.QLEM.SISRK.DYQQP.NQA....L.LE
Retrocopy AISKIHLR*QLEMNSISRKSDYQQP*NQANNMRLLLE

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_346 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_346 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	ENSAMEG00000005067	1 retrocopy	retro_amel_346 ,
Cavia porcellus	ENSCPOG00000002665	1 retrocopy	retro_cpor_1019,
Felis catus	ENSFCAG00000031243	1 retrocopy	retro_fcat_1312,
Pteropus vampyrus	ENSPVAG00000014829	1 retrocopy	retro_pvam_282,
Sorex araneus	ENSSARG00000008851	2 retrocopies	retro_sara_28, retro_sara_510,
Tupaia belangeri	ENSTBEG00000008608	1 retrocopy	retro_tbel_2485,