RetrogeneDB ID: retro_amel_1799

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194408.1:91592..92054(-)
• Located in intron of: ENSAMEG00000014061

Retrocopy information

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

Parental gene information

• Parental gene symbol: CUEDC2
• Ensembl ID: ENSAMEG00000017783
• Aliases: None
• Description: CUE domain containing 2 [Source:HGNC Symbol;Acc:28352]

Sequence

>retro_amel_1799
GACACCAAGGATGAATCAGCCAGTGCTGAGGAAGAGTTGCTTCCAGGTGTGCATGTACTCTTAGAGGTGTTCCCTCCTTA
TTCAGTGGAGCAGGCCCAGTGGATACTAGCAACAGCTCAGGGAGACTTGGAAGAATTTGTGCAAATGTTGGTAGAGGGGA
AGGAGGAGGGGACTCCAGCTTGGAATGGCCCCAACCAGGACCTGCCCAGATGCCTCAGAGGGTCCTTAAAAGGAACTGAA
ATGCTTCATCTTGCAGAAGTACATGATGGTGGATAACACAGAGTTTCAGGAGATTACCAGCGCATGGCTCCCAGGGAGGC
CCTCAAGAAGCTGATCCAATAAATCAACAACCAGATAGTGAGCACCAAAGGGGAGGGATTCAAAGATGTGCAGAACCCTG
AAGCCAAGGAGATGAAGGCCACATACATCAAACTCAAACTAGCCAGGAATTACCATTTCCAC

Alignment

ORF - retro_amel_1799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.8 %
• Parental protein coverage: 54.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DTQDEAAGAEEELLPGVDVLLEVFPTCSVEQAQWVLAKARGDLEEAVQMLVEGKEEGPPAWDGPNQDLPR
          DT.DE.A.AEEELLPGV.VLLEVFP..SVEQAQW.LA.A.GDLEE.VQMLVEGKEEG.PAW.GPNQDLPR
Retrocopy DTKDESASAEEELLPGVHVLLEVFPPYSVEQAQWILATAQGDLEEFVQMLVEGKEEGTPAWNGPNQDLPR

Parental  RLR-GPQKDELKSFILQKYMMVDSAEDQKI-HRPMAPREAPKKLIRYIDNQVVSTKGERFKDVRNPEAEE
          .LR.GP.K..LK.FILQKYMMVD..E.Q.I....MAPREA.KKLI..I.NQ.VSTKGE.FKDV.NPEA.E
Retrocopy CLR>GP*KE-LKCFILQKYMMVDNTEFQEI<YQRMAPREALKKLIQ*INNQIVSTKGEGFKDVQNPEAKE

Parental  MKATYINLKPARKYRFH
          MKATYI.LK.AR.Y.FH
Retrocopy MKATYIKLKLARNYHFH

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_1799 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1799 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017783	1 retrocopy	retro_amel_1799 ,
Bos taurus	ENSBTAG00000002501	1 retrocopy	retro_btau_757,