RetrogeneDB ID: retro_amel_1073

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192882.1:948301..949027(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000011989
• Aliases: None
• Description: None

Sequence

>retro_amel_1073
GCGTGCGCCCAGGCACAACTCCGCCCCTGGAAGCCGGGGCGCGCAGCCGCACTCCTTCTTGTACCCTTGGTGCTGCGTGC
GTCGCAGCGTGCAGCGGTGGCTCAGCCTGGACTTGAGGTAAGCCGCGGAGCGCTCACTGTCACAGTCTTCGGCTTAAAAA
GAAAAATTCTCCAGAGGATTTTGCAGCAATAGCTGGGCCCCTCAGGGTCACGCACTTACTGAACTTGAGCAACACAGGGA
ACAATGTTTAGTTTTAGCCCGTGCGCCTTCCAGAAAGCCCCACCTTGACTCTCCAGATCAACAAGCACACGCCGGTTGGT
GATGTCTCCTCGCTGCAGTGTGAGGCACCACATGTGTGAGCAGCTATCTGCCCACCGGCCCTCCTGGTGCTCCACAGCTT
CGGCCCCCACTGCGTGCACGTGCAGCTCCTGGCCACCATGTGCCAGACGCGGCTCCCCTCCATCAGCGTGCGCAAGGGGA
ACCAGAACACCATCCAGCATTGCCTTCTCATCAGCTACAACTCCACCCCCGGAGCGTCGTCACCACCATCATAGCGTCAG
AGTCGTTCCTGTGGGTGTAAGTCGTGGGATGATGGACGGTCTCCAGGAGAAATTCTCCAATACGAGCCACCTAATCGGTG
ATCTGCGGGCTACGGGTGCAGGACTATCAGAGAATGAGGCGGAGCGGGAAGGTGAGCCCCTGACGGAGCTGCCCCAGGCT
GTTGCC

Alignment

ORF - retro_amel_1073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.34 %
• Parental protein coverage: 53.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ARAQAQLRN-LEAYA-AQPHS--FVFARGRAGGVRQLSLDLRRVME-PLTAT-RLQIRKKNTLKDCVAVA
          A.AQAQLR..LEA.A.AQPHS........R....R.LSLDLR...E..LT.T..L...KKN...D..A.A
Retrocopy ACAQAQLRP<LEAGA<AQPHSFLYPWCCVRRSVQRWLSLDLR*AAE<ALTVT<SLRLKKKNSPEDFAAIA

Parental  GPLGVTHFLILSKTETNIYFKLMRLPGGPTLTFRINKYTLVRDVISSLRRHRMHEQQFAHPP-LLVLNSF
          GPL.VTH.L.LS.T..N..F...RLP..PTLT..INK.T.V.DV.SSL.....H......PP.LLVL.SF
Retrocopy GPLRVTHLLNLSNTGNNV*F*PVRLPESPTLTLQINKHTPVGDV-SSLQCEAPHV*AAICPPALLVLHSF

Parental  GPHGMHVKLMATMFQNLFPSINVHKVNLNAIKRCLLINYN-PDSQELDFRHYSIKVVPVGASRGMKKLLQ
          GPH..HV.L.ATM.Q...PSI.V.K.N.N.I..CLLI.YN.P........H.S..VVPVG.SRGM...LQ
Retrocopy GPHCVHVQLLATMCQTRLPSISVRKGNQNTIQHCLLISYN>PPPERRHHHH-SVRVVPVGVSRGMMDGLQ

Parental  EKFPNMSRLQDISELLATGAGLSESEAEPDGEHNITELPQAVA
          EKF.N.S.L..I..L.ATGAGLSE.EAE..GE...TELPQAVA
Retrocopy EKFSNTSHL--IGDLRATGAGLSENEAEREGE-PLTELPQAVA

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_1073 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1073 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 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011989	1 retrocopy	retro_amel_1073 ,
Loxodonta africana	ENSLAFG00000016399	4 retrocopies	retro_lafr_404, retro_lafr_588, retro_lafr_645, retro_lafr_666,