RetrogeneDB ID: retro_amel_1326

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193198.1:117907..118334(+)
• Located in intron of: ENSAMEG00000005263

Retrocopy information

• Ensembl ID: ENSAMEG00000005327
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000001600
• Aliases: None
• Description: None

Sequence

>retro_amel_1326
ATGACTTCTCATTGGGTTATTGGCATTTTCCTCCTCTCTGCTCTCCCCTTCTTGTGTCTGGAGCTTGGCATAGGATCCCT
GATCTAGGAATTAAAGATCTAATTTTGCTGTGTGTCTGGATTTTCTTACTGCTTGCTCTTCTTACTTTAATTATTTCTAT
GACTACCTTGTGGCTTAATTCATTTAAATCTTCCCAAGTGTATCTAAAAGAAAAAGAAGAGAAGAATGAGAAAAGGCAAA
AACTTGTCAGAAAAAACCAAGAAGCACAGGATGAAAAGGCCAGTAGATACATAAAGAATGTTCTAAAACCCCACCAGGAA
ATGAAATTCAGAAAACTGGAAGAGTCTTTTATCAGATGCTAGGTGAAACCTTGAAGTTAAGCAATGGTCATAAACTTGGG
GGTGATGAAGATTTGGTGCTGGAAAAC

Alignment

ORF - retro_amel_1326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.08 %
• Parental protein coverage: 52.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASRGIVGIFLLAALPLLCLELRRG-IPDLGKCWLFLSGTLFVFLSRLLNSFLLSVVNGWLFTLVSDSSH
          M.S....GIFLL.ALP.LCLEL..G.IPDLG...L.L......FL...L.....S....WL....S....
Retrocopy MTSHWVIGIFLLSALPFLCLELGIG<IPDLGIKDLILL-CVWIFLLLALLTLIISMTTLWLNSFKSSQVY

Parental  VLEEEEKNEKRQKLVRKKQQEAQGEKATRYIENVLKPHQEMKLRKLEER-FYQMTGETWKLSNGHKLGQG
          .............LVRK.Q.EAQ.EKA.RYI.NVLKPHQEMK.RKLEE..FYQM.GET.KLSNGHKLG.G
Retrocopy XXXXXXXXXXXXXLVRKNQ-EAQDEKASRYIKNVLKPHQEMKFRKLEES<FYQMLGETLKLSNGHKLG-G

Parental  DEDLVLED
          DEDLVLE.
Retrocopy DEDLVLEN

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_1326 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1326 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001600	2 retrocopies	retro_amel_1272, retro_amel_1326 ,
Choloepus hoffmanni	ENSCHOG00000006159	4 retrocopies	retro_chof_1161, retro_chof_1175, retro_chof_1383, retro_chof_1500,
Myotis lucifugus	ENSMLUG00000016846	1 retrocopy	retro_mluc_606,