RetrogeneDB ID: retro_amel_119

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193687.1:472732..474610(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000020105
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKTL1
• Ensembl ID: ENSAMEG00000018441
• Aliases: None
• Description: None

Sequence

>retro_amel_119
ATGGCAGACGACTCCACGCCCGACGCGAACACCGTGCAGGCGCTGCGGGACGTGGCCAACCGCCTGCGAATCCATTCCAT
CAGGGCCACGTGTGCAGCCAGCTCCGGCCACCCCACTTCGTGCTGCAGCGCCGCTGAGATCATGTCGGTGCTCTTTTTCC
ACACCATGAGGTATAAACGGACGGACCCGGAACACCCCGACAATGACCGATTCATCCTGTCCAAGGGCCATGCTGCTCCA
ATCCTCTATGCTGCCTGGGCAGAGGTGGGCAACATCGGCGAATCCGACTTGCTGAGCTTGAGGAAAATTCACTGTGACCT
GGAGGGACATCCCACCCCAAGGCTGCCATTTGTTGACGTGGCAACAGGATCACTTGGGCAAGGATTAGGTGCCGCGTGTG
GAATGGCGTACACTGGCAAGTATTTTGACAAGGCCAGCTACCGGGTGTTCTGCCTCCTGGGGGATGGCGAATCCTCAGAA
GGCTCTGTCTGGGAGGCTCTGGCCTTCGCTTCTCACTACGGGTTGGACAATCTGGTGGCCGTCTTCGACGTGAACCGCTT
GGGACAAAGTGGAGTCACGCCTCTTGAGCACTGCACAGACATCTATCAGAATCGCTGTGAAGCCTTTGGGTGGAATACCT
ACTTGGTGGATGGCCATGATGTGGAGGCATTATGCCAAGCGTTTTGGCAAGCAGCTCAAGTGAAGAACAAGCCCACTGCC
ATCATTGCGAAGACCTTCAAGGGCCGAGGTATTCCAAATATTGAGAATGCAGAACATTGGCATGGAAAGCCGATGCCAAA
AGAAAGAGTGGATGCAATCATCAAAGTAATTGAGAGTCAGATACAGAGCAACAGGAATCTCACACCAAAACCTCCCGTTG
AAGACTCACCTCAAATCAGCATCAGGAATGTGAAAATGACCTGTCTGCCTGATTATGTAGTTGGAGACAGGATAGCTACT
AGGAAAGCATATGGTTTGGCTTTGGCTAAACTGGGCCACGCAAATGAAAGAGTTATTGTCTTGGCTGGTGATACAAAGAA
CTCCACCTTTTCTGAGATATTCAATGAAGAACACCCTGACCGTTTTATTGAGTGTTTTACCGGGGAGCAAAACATGGTGA
GTGTGGCACTAGGCTGTGCCACACGTGGTCGAACCATTGCTTTTGTTAGCACCTTTGCTGCCTTTTTGACCCGAGCATTT
GATCAGATACGGATGGGAGCCATATCTCAAACCAATATCAATTTTATTGGTTCCCACTGTGGGGTATCCATTGGTGAAGA
TGGACCCTCCCAGGTGGCCCTGGAGGACCTAGCCATGTTCCGAAGCATTCCCAATTGTACTGTTTTCTATCCAAGTGATG
CTATCTCAACAGAGTATGCTGTTTATCTGGCTGCCAATACCAAAGGAATGTGTTTCATTAGGACCAGCCAAACAGAAACT
GCAGTTATTTATACCCCACAAGAAAATTTTGAGATTGGACAGGCCAAGGTCATCCGCCAGAGTGTCAATGACAAAGTCAC
AGTTATTGGAGCTGGAGTTACTCTGCATGAAGCCTTAGCAGCTGCTGACAGTCTTTCTCAACAAGGTATTTCTATCCGTG
TCATTGACCCATTTACCATTAAACCCCTGGATGCTGCCAACATCATCTCCAGTGCAAAAGCTACAGGTGGCCAGGTTATC
ACAGTGGAGGATCACTACCGGGAAGGTGGCATTGGCGAAGCTGTATGTGCGGCCGTCTCTGGGGAGCCTGACATCCTTGT
TCAGCAGCTAGCAGTGTCAGAAGTGCCTCAGTGTGGGACACCTAGTGAATTGCTGGATAAATTTGGAATCAGTGCCAGAC
ACATCATAGCAGCTGTGAAAAATACTTTAATGAGCTAA

Alignment

ORF - retro_amel_119 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 86.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLSFVDVATGWLGQGLGAACGMAYTGKYFDKASYRVFCLMGDGESSEGSVAWEALAFASHYNLDNLVAIF
          .L.FVDVATG.LGQGLGAACGMAYTGKYFDKASYRVFCL.GDGESSEGSV.WEALAFASHY.LDNLVA.F
Retrocopy RLPFVDVATGSLGQGLGAACGMAYTGKYFDKASYRVFCLLGDGESSEGSV-WEALAFASHYGLDNLVAVF

Parental  DVNRLGHSGALPLEHCIDVYQKRCEAFGWNTYVVDGRDVEALCQVFWQASQVKNKPTAVVAKTFKGRGIP
          DVNRLG.SG..PLEHC.D.YQ.RCEAFGWNTY.VDG.DVEALCQ.FWQA.QVKNKPTA..AKTFKGRGIP
Retrocopy DVNRLGQSGVTPLEHCTDIYQNRCEAFGWNTYLVDGHDVEALCQAFWQAAQVKNKPTAIIAKTFKGRGIP

Parental  SVEDAENWHGKPMPKERADAIIKLIESQIETDKNLEPKRPIEDAPQINIMDIEMGSPPAYKVGEQIATRK
          ..E.AE.WHGKPMPKER.DAIIK.IESQI....NL.PK.P.ED.PQI.I....M...P.Y.VG..IATRK
Retrocopy NIENAEHWHGKPMPKERVDAIIKVIESQIQSNRNLTPKPPVEDSPQISIRNVKMTCLPDYVVGDRIATRK

Parental  ACGLALAKLGHANDRVIVLDGDTKNSTFSDMFKREHPERFIECFIAEQNMVSVALGCATRGRTVAFASTF
          A.GLALAKLGHAN.RVIVL.GDTKNSTFS..F..EHP.RFIECF..EQNMVSVALGCATRGRT.AF.STF
Retrocopy AYGLALAKLGHANERVIVLAGDTKNSTFSEIFNEEHPDRFIECFTGEQNMVSVALGCATRGRTIAFVSTF

Parental  AAFFTRAFDQIRMGAISQININLIGSHCGVSVGEDGPSQMALEDLAMFRSVPNCTIFYPSDAISTEHAVL
          AAF.TRAFDQIRMGAISQ.NIN.IGSHCGVS.GEDGPSQ.ALEDLAMFRS.PNCT.FYPSDAISTE.AV.
Retrocopy AAFLTRAFDQIRMGAISQTNINFIGSHCGVSIGEDGPSQVALEDLAMFRSIPNCTVFYPSDAISTEYAVY

Parental  LAANTKGMCYIRTSRPETAVIYTPQESFAIGQAKVVRQSVNDKVTVIGAGVTLHEALAAAENLSKEDISI
          LAANTKGMC.IRTS..ETAVIYTPQE.F.IGQAKV.RQSVNDKVTVIGAGVTLHEALAAA..LS...ISI
Retrocopy LAANTKGMCFIRTSQTETAVIYTPQENFEIGQAKVIRQSVNDKVTVIGAGVTLHEALAAADSLSQQGISI

Parental  RVIDLFTIKPLDVATIVSNAKATGGRIITVEDHYPEGGIGEAVCAAVSMEPDILVHQLAVPGVPRSGNPS
          RVID.FTIKPLD.A.I.S.AKATGG..ITVEDHY.EGGIGEAVCAAVS.EPDILV.QLAV..VP..G.PS
Retrocopy RVIDPFTIKPLDAANIISSAKATGGQVITVEDHYREGGIGEAVCAAVSGEPDILVQQLAVSEVPQCGTPS

Parental  ELLDLYGVSARHIIVAVKCILMN
          ELLD..G.SARHII.AVK..LM.
Retrocopy ELLDKFGISARHIIAAVKNTLMS

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_119 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_119 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018441	1 retrocopy	retro_amel_119 ,
Equus caballus	ENSECAG00000021992	1 retrocopy	retro_ecab_6,
Felis catus	ENSFCAG00000011392	1 retrocopy	retro_fcat_84,
Loxodonta africana	ENSLAFG00000005145	1 retrocopy	retro_lafr_6,
Pongo abelii	ENSPPYG00000020870	1 retrocopy	retro_pabe_205,
Ictidomys tridecemlineatus	ENSSTOG00000005014	1 retrocopy	retro_itri_30,