RetrogeneDB ID: retro_amel_1547

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193587.1:174569..175335(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ILK
• Ensembl ID: ENSAMEG00000016283
• Aliases: None
• Description: integrin-linked kinase [Source:HGNC Symbol;Acc:6040]

Sequence

>retro_amel_1547
ACAGAGAACAACCTCAACCAGGGGGATGATCATGGCTTCTCCCCCTTGCACTGGGCCTTCCAAGAGGGCTGTTCTGCTGT
GGTTGAAATGCTGATCATGCGGGGGACATGAATCGATGTGATGAACCGTGGGAATGACGCCCCCTGCACCTGACAGCCAG
TCATGGACACCATGATGTTGTGCAGGAGCTGCTGCAGTATAAAGCTGACATCAATGCAGTGAAAAAGCATGGAAATGTGC
CCCTGCACTATGCCCATTTTGGGGGCCAAGATTGGGTTGCAGAGGACCTGTTGACTAATGGGGCCCTTGTCAGCATTTAT
AACAAGTACGGAGAAATGCCTGTGGACAAATCAAAGCACCCCTGAGAGAGCTCCTCCGAGAGTGGGCAGAGAAGATGGGC
CACAACCTTAACCATATTCCATACAAGGACACATTCTGGAAGGGAAACACCCGCACTCAACCCTGAAATGTGACTCTGAA
CAAACACTCTGGCATTGACTTCAAACAGCTCAACTTTCTGGCAAAGTTCAACGAGAATCACTCTGGAGAGCTATGGAAGG
GACATTGGCAGGGCGATGACATGCTCGTGAAGGTGCTTAAGTTTCGAGACTGGCGTACAAGGAAGAGCAAGTACCTCATT
GAGGAGTGTCCCTGTCTCGGGATTTTCTCGCGTCCAAATGTGTCCCCAGTGGTAGGTGCCTGTCAGTCTTCACCTCCTCC
TCACCCCACCCTCATCACACACTGGATACCGTATGGATCACTGTAC

Alignment

ORF - retro_amel_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.23 %
• Parental protein coverage: 56.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TENDLNQGDDHGFSPLHWACREGRSAVVEMLIMRGARINVMNRGDDTP-LHLAASHGHRDIVQKLLQYKA
          TEN.LNQGDDHGFSPLHWA..EG.SAVVEMLIMRG..I.VMNRG.D.P.LHL.ASHGH.D.VQ.LLQYKA
Retrocopy TENNLNQGDDHGFSPLHWAFQEGCSAVVEMLIMRGT*IDVMNRGNDAP<LHLTASHGHHDVVQELLQYKA

Parental  DINAVNEHGNVPLHYACFWGQDQVAEDLVANGALVSICNKYGEMPVDKAK-APLRELLRERAEKMGQNLT
          DINAV..HGNVPLHYA.F.GQD.VAEDL..NGALVSI.NKYGEMPVDK.K.APLRELLRE.AEKMG.NL.
Retrocopy DINAVKKHGNVPLHYAHFGGQDWVAEDLLTNGALVSIYNKYGEMPVDKSK<APLRELLREWAEKMGHNLN

Parental  RIPYKDTFWKGTTRTRPRNGTLNKHSGIDFKQLNFLAKLNENHSGELWKGRWQGNDIVVKVLKVRDWSTR
          .IPYKDTFWKG.TRT.P.N.TLNKHSGIDFKQLNFLAK.NENHSGELWKG.WQG.D..VKVLK.RDW.TR
Retrocopy HIPYKDTFWKGNTRTQP*NVTLNKHSGIDFKQLNFLAKFNENHSGELWKGHWQGDDMLVKVLKFRDWRTR

Parental  KSRDFNEECPRLRIFSHPNVLPVLGACQSPPAPHPTLITHWMPYGSLY
          KS....EECP.L.IFS.PNV.PV.GACQS.P.PHPTLITHW.PYGSLY
Retrocopy KSKYLIEECPCLGIFSRPNVSPVVGACQSSPPPHPTLITHWIPYGSLY

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_1547 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1547 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	ENSAMEG00000016283	1 retrocopy	retro_amel_1547 ,
Mustela putorius furo	ENSMPUG00000005495	1 retrocopy	retro_mputfur_1297,
Mus musculus	ENSMUSG00000030890	1 retrocopy	retro_mmus_1119,