RetrogeneDB ID: retro_amel_1352

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193237.1:803122..803764(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBR4
• Ensembl ID: ENSAMEG00000013400
• Aliases: None
• Description: carbonyl reductase 4 [Source:HGNC Symbol;Acc:25891]

Sequence

>retro_amel_1352
CTCTGGGGAGGCTCCCAGGGCACTGGCAGGGCACTGGCCCAATTAATGGCCAGAAAGTCTACCAATTGGCCATCATCCCC
AGGACTCTGGAAGTGGCCAAAGCCCCTGGAGCTGGTGACCTTGGTGGAGGTCATTTGTCATTTAGCTATGATGCTGCCAA
AGAATGTAAGGCTCAAAATACATTTGAAGAGATGGAGAAAAAAATTGGGTCAAGTTTATCTCTTGGTAAATGCAGCTGGA
ATTAACAGGGACAGCATTTTAGTAAGAACAAAACCTGAAGGTATGGTATCTCAGCACACACTACTCTCTTGGGCTCCATG
CTGACTTGGAAAGCTGCCAGGAAGACTATGATTCAACGCCAGAGAGGGTCTATTGTTACTGTAGGATGCATTATTGGCTT
AAAAGGCCATTCTGGCCAATGTGTGTACAGTGCCAGTAAAGGAAGATTCTTTGAATTTGCACATACTCCTGCTAAAGGAG
TAACAAGAAAGAAAATTACAGTGAATGTAGTTGTACCAGGATTGGTTCACACAGAGAGGATGAAAGACTTAAACATTTAA
AGAAAAATACCTCTCTGGGGAAGTTTGGAGAACCTATTAATGTGCACATGATATTGTGTTTCTTTTGGAAGCACAATATA
TG

Alignment

ORF - retro_amel_1352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.22 %
• Parental protein coverage: 91.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VFGGSRGIGRAVAQLMA-QKGYRLAIVARNLEVARA-AAGDLGGSIGDHLAFSCDVAEERDVQNTFEEME
          ..GGS.G.GRA.AQLMA.QK.Y.LAI..R.LEVA.A..AGDLG...G.HL.FS.D.A.E...QNTFEEME
Retrocopy LWGGSQGTGRALAQLMA<QKVYQLAIIPRTLEVAKAPGAGDLG---GGHLSFSYDAAKECKAQNTFEEME

Parental  KK-LGRVNFLVNAAGINSRDSLLVRTKTEDMISQ-LHTNLLGSMLTCKVALKTMIQQQRGSIVNVGSVIG
          KK.LG.V..LVNAAGIN.RDS.LVRTK.E.M.SQ..HT.LLGSMLT.K.A.KTMIQ.QRGSIV.VG..IG
Retrocopy KK>LGQVYLLVNAAGIN-RDSILVRTKPEGMVSQ<AHTTLLGSMLTWKAARKTMIQRQRGSIVTVGCIIG

Parental  LKGNSGQSVYSAGKGGLVGFSRALAKEVARKKIRVNVVAPGFVHTDMTKDLKEEHLKKNIPL-GRFGEPI
          LKG.SGQ.VYSA.KG....F....AK.V.RKKI.VNVV.PG.VHT...KDL........IPL.G......
Retrocopy LKGHSGQCVYSASKGRFFEFAHTPAKGVTRKKITVNVVVPGLVHTERMKDL---NI*RKIPL>GEVWRTY

Parental  DVAHAVVFLLESPYI
          ..AH..VFLLE..Y.
Retrocopy *CAHDIVFLLEAQYM

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_1352 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1352 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371,
Ailuropoda melanoleuca	ENSAMEG00000013400	1 retrocopy	retro_amel_1352 ,
Canis familiaris	ENSCAFG00000007520	1 retrocopy	retro_cfam_1341,
Felis catus	ENSFCAG00000030280	1 retrocopy	retro_fcat_885,
Oryctolagus cuniculus	ENSOCUG00000006446	1 retrocopy	retro_ocun_1883,
Tursiops truncatus	ENSTTRG00000000258	1 retrocopy	retro_ttru_1855,