RetrogeneDB ID: retro_amel_1911

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195723.1:16384..16900(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAZ
• Ensembl ID: ENSAMEG00000014864
• Aliases: None
• Description: None

Sequence

>retro_amel_1911
GTGACAGTGACCCCCTCTGGAAAGCACCTGGAGGAAGCATGCTTGTGAGAGGTGCAGCAAGGCCTTCAGCGATGTCTCCC
ATCCAAATGACCGGGGCTGGAGCACTGGGACTAGGAGCCCCACCCATGCCCAGTGTGCCAGCAGTGCACAAGCACAAGGA
CCCCATGAGCTGTCACAAACACACAGAATACAGGCGCAGTGCACAAGCCCTACAACTGTTCACACTGTGGCCAGAGCAGC
TCCCGCAGGATCACCTCATCAGTCATGCTCACCGTGCGCTCCACAGACAGCCCTTCACATGTGACGTGTGTTGCAGTTTT
TGCTCCGAAGGATCTACTGCAGCACACACAGAACCGCACGAGGACAGGTGCAGGGTCACGTGTGTGGCAAGATGCTAAGC
ACGGCTGCTATTTCCCACCACGTGCAGATGTGCTGCCAGGATGTCACCGTGTCTGTGAGCTCCGCAGCAGAGGTACTGGT
GAGCTCTGTCCCAGGACAGCAGTGGTGACTGTGGCC

Alignment

ORF - retro_amel_1911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.72 %
• Parental protein coverage: 58.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  VTTTASGKRI-RKNHACEMCGKAFRDVYHLNRHK-LSHSDEKPYQCPVCQQR-FKRKDRMSYHVRS-HDG
          VT.T.SGK...RK.HACE.C.KAF.DV.H.N....L.H.D..P..CPVCQQ...K.KD.MS.H......G
Retrocopy VTVTPSGKHL>RK-HACERCSKAFSDVSHPNDRG<LEHWD*EPHPCPVCQQC<HKHKDPMSCHKHT>NTG

Parental  AVHKPYNCSHCGKSFSR-PDHLNSHV-RQVHSTERPFKCEKCEAAFATKDRLRAHTVRHEEK-VPCHVCG
          AVHKPYNCSHCG.S.SR..DHL.SH..R..H....PF.C..C...F.......AHT..HE...V..HVCG
Retrocopy AVHKPYNCSHCGQSSSR<QDHLISHAHRALH--RQPFTCDVC-CSFCSEGSTAAHTEPHEDR<VQGHVCG

Parental  KMLSSAYISDHMKVHSQ-GPHHVCELCNKGTGEVCPMAAAAAAA
          KMLS.A.IS.H.....Q.G.H.VCEL...GTGE.CP..A....A
Retrocopy KMLSTAAISHHVQMCCQ<GCHRVCELRSRGTGELCPRTAVVTVA

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_1911 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1911 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014864	1 retrocopy	retro_amel_1911 ,