RetrogeneDB ID: retro_amel_1297

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193165.1:779051..780117(-)
• Located in intron of: ENSAMEG00000015683

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO15
• Ensembl ID: ENSAMEG00000013571
• Aliases: None
• Description: F-box protein 15 [Source:HGNC Symbol;Acc:13617]

Sequence

>retro_amel_1297
GCAGACAGTGCTTCTATGAGGCAGTGCGCGAGGCAGGGAAAGCACTGTGAGAAGTCCTCCGCTAACCTTTCTGTGTCTCT
GGATAGTACGCCTTCAGAAATCTTGCGAAGATCTTTTCCCACTTGGATGCCGGGACCTGCTGTGTGCTGGATGTGTGAAT
AGGCTCTTTCATCATCTGGCCAATGACCTTTTTATTTGGATCAGAATCTCTTCAACTGCCTTTTCACCTAAAAGATCTAA
TTGGAAAGTTATTTCAGCAGAGAAGACCGTTGTATCTACGAACTTACTATCAGTCGAGGGTAAAGAACGTGGGTATTGGA
AGAAAGAATCTATCACAGAACAAAGAGCATCTGCAAAAACAGCACTCGCTCAGGTTCTCAAACCTGTCAACCCTTACACA
GGCCTTCCAGTTCAAACCTAAGAGGCCCTCAGAATATCTGGGTTAGGTCGGGTGATTATATTGAAAGAAAAAAGTGGAAA
AGAATACATCATGGAGTGCATTGACCTTTCCTTAAATGATTCATCAGTGACGATTATGTGGTATGGCCAGAATTTGCCAC
AGCTAGCCACATTGTCAACTTTAGATTTGTGTGGTATGACACTAGTTTTGTGAACCAGTCTCCAACCCCCTCCAAAAACA
GGCCTCGGTGGCATTCTTTAGTTGCAAAGTATCACCTGAGTAACTTAACTGAATCCACCATGATGGCTGGGACAGACTCA
TTCGGGTCTTCTGCTTACACCCAGGCCTCCTGGTGGGGCTGTGGAAGAGGGAGGAAGAACTGGCTTTTGTTACAGCAGAT
CTTCATTTCCATCACTTTGTGGAAAAGAGCACATTAGGCTCAGCCACTGTCCCCTATGAGCTATGTCCTCACACCCCCTT
TTGGATGACAACCCGGAGTATGGACTGCATGGCTACCAACTCCATGCTGATATGCACAGCAGTGGAATTTTCTACCTGCG
TGGCACATTTCTCAATCTCTTTACCAAGAAAGGATACATTGAAAATGGATATGTGAAGCTTGTTGTTGTAAGTTTTAAAA
ATAACACAGAACAGCTACCAATAGTA

Alignment

ORF - retro_amel_1297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.28 %
• Parental protein coverage: 77.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AGNTALRQCAGRGKCCELPSTRSPVSLESIPSEIL-LKIFSYLDAVT-LLCTGCVNRHFYHLANDNFIWI
          A.....RQCA..GK.CE..S....VSL.S.PSEIL..KIFS.LDA.T.LLC.GCVNR.F.HLAND.FIWI
Retrocopy ADSASMRQCARQGKHCEKSSANLSVSLDSTPSEIL<AKIFSHLDAGT<LLCAGCVNRLFHHLANDLFIWI

Parental  RIYSTAFSPKRSNWKVNSAEKTAVSMNSLSVEDKEPGYWKKEYITKQRASVKAALAQVLKPVNPYTGLPV
          RI.STAFSPKRSNWKV.SAEKT.VS.N.LSVE.KE.GYWKKE.IT.QRAS.K.ALAQVLKPVNPYTGLPV
Retrocopy RISSTAFSPKRSNWKVISAEKTVVSTNLLSVEGKERGYWKKESITEQRASAKTALAQVLKPVNPYTGLPV

Parental  QTKEALRISGLGWVIILKEKNGREYIMEHIDLSINDSSVTIMWYGKTWPQLATLSTLDLCGVTPL-FMDR
          QT.EALRISGLG.VIILKEK.G.EYIME.IDLS.NDSSVTIMWYG...PQLATLSTLDLCG.T...F...
Retrocopy QT*EALRISGLGRVIILKEKSGKEYIMECIDLSLNDSSVTIMWYGQNLPQLATLSTLDLCGMTLV<FVNQ

Parental  SKTPSKNGPRWHSLIAKYNLSNLTESTMI-GWDRLIRIFCLHPGLLVGLWKGEEELAFVMANLHFHHLVE
          S.TPSKN.PRWHSL.AKY.LSNLTESTM..GWDRLIR.FCLHPGLLVGLWK.EEELAFV.A.LHFHH.VE
Retrocopy SPTPSKNRPRWHSLVAKYHLSNLTESTMM<GWDRLIRVFCLHPGLLVGLWKREEELAFVTADLHFHHFVE

Parental  KSTLGSATVPYELPPHT-PLLDDSPEYGLHGYQLHVDMHSSGIFCLCGTFRNLFTKKGSIENGYVKLVVI
          KSTLGSATVPYEL.PHT.PLLDD.PEYGLHGYQLH.DMHSSGIF.L.GTF.NLFTKKG.IENGYVKLVV.
Retrocopy KSTLGSATVPYELCPHT<PLLDDNPEYGLHGYQLHADMHSSGIFYLRGTFLNLFTKKGYIENGYVKLVVV

Parental  SFKNNTEHLPLI
          SFKNNTE.LP..
Retrocopy SFKNNTEQLPIV

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_1297 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1297 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013571	1 retrocopy	retro_amel_1297 ,
Tarsius syrichta	ENSTSYG00000012653	1 retrocopy	retro_tsyr_2142,