RetrogeneDB ID: retro_amel_895

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192721.1:299768..300625(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000000147
• Aliases: None
• Description: None

Sequence

>retro_amel_895
ATGATATCTATTCACGTGATGGCACTGACCCTGCTGACACCCATGGGACCATTCTTGAGTGCTCCAAGTTTAGCAACACA
GAGGTGTTCCAGGCAGTGCAGGTGCACCTGGGCTGCCTTGGTCAACCTCATCATCACCCTGCAGTGTGTGCCCCAGTTCG
ACTTGCAGGAGATCTCCCTCCCCTCAATCCTGAAAGAGGTTCTTGACAACCTGGACAGCCACCTGAGGAAATCTGAATTC
TTCCACTTCCTTTGGTTCTCACGCAGTGAGAACGTCAGCATCATCTACTGGGACCACACCAAAAAGTCCCCCTTCTCTTC
AGCCAACTGGTTTTGGGACTATGCCATCAAATTCTATTTACTGAAGTTCTTTCTCTGGATCAGTTCCTTCTGCTGGGCCT
TTGTCGGCTGGATCAATCGCTTCTTCTTCTAGCTCCTGTTCATCAGGAAGGAGAGTAGCAACGTCAGCCACAAGATCTTC
ACCCACGAGTGCTGCTTCAAGCAGCATGTCCAGGACAGGGCCATCCCCAGATAGAAGACCAAGGAGATCCTGATGGAACT
GAAAGCCATCCTGGAGACCTACCCCAAGATGATGGCTCACTACCCTGTAGAGCCGCTTCATCTCCGGGGGATGATATCTT
GCTGAGTTCCTGTTTCCAGAGGGACAGCTGCTACATGAACATCATTATGTGCAGAGCCTATGGCAAGGAAGTATCACAGC
TGGACTACTGTCTGGCCTAGGAGACCATCAGGAAGACAGTGAGGGGCAAGCCCCATTGGGCTAAGGCCCACAAATCTGCC
TGGAGGGACTTAGAAAATGTATCTAGCCTCTTCGTAGTTCTGTGCCATCTGAGAAAG

Alignment

ORF - retro_amel_895 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.01 %
• Parental protein coverage: 66.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILATQVVALTLLTADGTILECSESSNADVFQAARVHLGCLGVILTITLQCVPQFHLHEISFPSTLEEVLN
          .....V.ALTLLT..G..L..............R.....L.V.L.ITLQCVPQF.L.EIS.PS.L.EVL.
Retrocopy MISIHVMALTLLTPMGPFLSAPSLATQRCSRQCRCTWAAL-VNLIITLQCVPQFDLQEISLPSILKEVLD

Parental  NLDSHLKKSEYFRFLWFPHSENVSVIYQDHTNKPPSSSANWFWDYAIGFYLLEFLLWISSFLPGLVGWIN
          NLDSHL.KSE.F.FLWF..SENVS.IY.DHT.K.P.SSANWFWDYAI.FYLL.F.LWISSF....VGWIN
Retrocopy NLDSHLRKSEFFHFLWFSRSENVSIIYWDHTKKSPFSSANWFWDYAIKFYLLKFFLWISSFCWAFVGWIN

Parental  RFFFWLLFTRKKESSNLSHKIFTYECRFKQHVQDWAIPREKTKEALLELKAMLEAHPKMVAHYPVEVRFT
          RFFF.LLF.R.KESSN.SHKIFT.EC.FKQHVQD.AIPR.KTKE.L.ELKA.LE..PKM.AHYPVE....
Retrocopy RFFF*LLFIR-KESSNVSHKIFTHECCFKQHVQDRAIPR*KTKEILMELKAILETYPKMMAHYPVEPLHL

Parental  R-GDDILLSPCFQRDSCYMNIIMYRPYGKDVPRLDYWLTYETIMKKVGGRPHWAKAHNCTRKDFEKMYPA
          R.GDDILLS.CFQRDSCYMNIIM.R.YGK.V..LDY.L..ETI.K.V.G.PHWAKAH.....D.E.....
Retrocopy R<GDDILLSSCFQRDSCYMNIIMCRAYGKEVSQLDYCLA*ETIRKTVRGKPHWAKAHKSAWRDLENVSSL

Parental  FSKFCAIRE
          F...C..R.
Retrocopy FVVLCHLRK

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_895 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_895 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000147	1 retrocopy	retro_amel_895 ,
Canis familiaris	ENSCAFG00000008414	1 retrocopy	retro_cfam_1517,
Felis catus	ENSFCAG00000023835	1 retrocopy	retro_fcat_1263,