RetrogeneDB ID: retro_amel_1850

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194833.1:4750..5786(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIM27
• Ensembl ID: ENSAMEG00000013863
• Aliases: None
• Description: tripartite motif containing 27 [Source:HGNC Symbol;Acc:9975]

Sequence

>retro_amel_1850
GGGGCTGAGATGGTTGTGTGTGAGAAGCACCACAACCCCCTGAAGGTGTACTGTGAGGTGGACCAGATGCCCATCTGCAT
GGTGTGTAGCTGCTTCTGCAAGCACACTAGCCAAGCATGGTGCAGCTCAAGGAGGTGGTGGAGGGTTTCAAGGAGCAAAT
CAAGAACCAGCTGGACCACATGGAAAGACTGAAAACTTAAAAAAGAGGCATGGGCATAGCAGGAGCAGAGGAGCTGAACT
CTTGAGCCTGAACCAGATGGAGAGAGAGATCATCTGGAAGTTTGAGCAGCTGTCTCACTCCTTGAAGCATCATGAGTATC
GCCTCCTGGCCCACCTTGAAGAGCTAGATTTGGAAATCTACAACAACATCAATGGTGCCAACACCAGATCTGCTGCGTCT
CCCACCCAGGTAGCCTGATCACCCAGCTGGAAGAGAAGCAGCAGCAGCTTACCAGGGAGCTCCAACAGGACACTGGGGAC
ACACCGAGCAGACCTGAAAGAATCAGGATCCCTGAACTCTGGATCACACCTCCAGATCTGTGAGAGAAAGTCTACATTTT
CACTCAAAACTCTCTGTTCTTGACTGAAAGTTTGAGGCAGTTCACAGAAAACAAACAGTCAATATGGGGAAAATCCAAGA
ATTGAGAAAGGCTCAATTATACTCAGTATATGTGACTCTGGACCCAGACACAGCCTATCCCAGTTTGATCCTTTCCTGCA
GCATGTGTGCAAGGCACAGTTACTTCTAGCAGGACCTGCCTTACAATCCAGAGCTGTTAAATCTGTCCCCCCATGTCTTG
GGTTCTCAAGATTAATCACTGGGAGACATTATTGGGAGGTAGATATGAGAGATAAAGCCGAGTGAACCATAGGTGCATGT
GAAAACTCAATGTGCAGAAAAAGGTGGAGTAATTTTGGGCATCCAGAATGGATTCTGGGCAGTGTCCTTGTGGTTGGGAA
AGATTACTGGGCTCTTTATACCTCCCCAGTGACTGCCCTTCCCCAGCAGACTGCTCTCCAGTGGGGGGGAGGATTT

Alignment

ORF - retro_amel_1850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.48 %
• Parental protein coverage: 62.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GGEMGVCEKHREPLKLYCEEDQMPICVVCDRSREHRGH-SVLPLEEAVEGFKEQIQNQLEHLKRVK-DLK
          G.EM.VCEKH..PLK.YCE.DQMPIC.VC.....H....S...L.E.VEGFKEQI.NQL.H..R.K..LK
Retrocopy GAEMVVCEKHHNPLKVYCEVDQMPICMVCSCFCKHTSQ<SMVQLKEVVEGFKEQIKNQLDHMERLK<NLK

Parental  KRRRAQGEQARAELLSLTQMEREKIVWEFEQLYHSLKEHEYRLLARLEELDLAIYNSINGAIT-QFSCNI
          KR.........AELLSL.QMERE.I.W.FEQL.HSLK.HEYRLLA.LEELDL.IYN.INGA.T.Q..C..
Retrocopy KRH-GHSRSRGAELLSLNQMERE-IIWKFEQLSHSLKHHEYRLLAHLEELDLEIYNNINGANT<QICC-V

Parental  SHLSGLIAQLEEKQQQPTRELLQDIGDTLSRAERIRIPEPWITPPDLQEKIHIFAQKCLFLTESLKQFTE
          SH...LI.QLEEKQQQ.TREL.QD.GDT.SR.ERIRIPE.WITPPDL.EK..IF.Q..LFLTESL.QFTE
Retrocopy SHPGSLITQLEEKQQQLTRELQQDTGDTPSRPERIRIPELWITPPDL*EKVYIFTQNSLFLTESLRQFTE

Parental  KMQS-DMEKIQELREAQLYSVDVTLDPDTAYPSLILSDNLRQVRYSYLQQDLPDNPERFNLFPCVLGS-P
          ..QS..M.KIQELR.AQLYSV.VTLDPDTAYPSLILS......R.SY..QDLP.NPE..NL.P.VLGS..
Retrocopy NKQS<NMGKIQELRKAQLYSVYVTLDPDTAYPSLILSCSM-CARHSYF*QDLPYNPELLNLSPHVLGS<S

Parental  CFIAGRHYWEVEVGDKAKWTIGVCEDSVCR-KGGVTSAPQNGFWAVSLW-YGKEYWAL-TSPMTALPLRS
          ..I.GRHYWEV...DKA..TIG.CE.S.CR.KGGV....QNGFWAVSLW..GK.YWAL.TSP.TALP...
Retrocopy RLITGRHYWEVDMRDKAE*TIGACENSMCR>KGGVILGIQNGFWAVSLW<VGKDYWALYTSPVTALPQQT

Parental  PLQRVGIF
          .LQ..G.F
Retrocopy ALQWGGGF

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_1850 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1850 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	ENSAMEG00000013863	1 retrocopy	retro_amel_1850 ,