RetrogeneDB ID: retro_amel_1328

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193200.1:145616..146709(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATL1
• Ensembl ID: ENSAMEG00000009965
• Aliases: None
• Description: atlastin GTPase 1 [Source:HGNC Symbol;Acc:11231]

Sequence

>retro_amel_1328
TTGAGAGATTTAGCCACAATATTTGTCCTTGGCAAAATGATAAGTTTAATATAGGTATATATCCTATCCCAAATGTCCAA
GAGGATGATCTTCAGAATCTTCAGCTTTTTGCTGAGTATGGCCAACTGGCAGGGAGGCAACATTCCTGAAGCCATTTCAA
AGCCTGACATTTTTCATTGAGAACTGAAGTTACCCAATTGAATTTGGGGAAGCCAATGGTGGCACCAAATTTTTGGGAAA
CTTCCTAAAGTTTTCAGAGAACCAACATGAAGAACTACAGAATGTTTGAAAACACTCCTATTTCTGTTTCACCAAAATAT
ACTGTTTTCTGCTACCTGGTCATGGCTTAAAGGTAGTTCCCAATCTACACTTTGATGGAAAATTTAAAGAAATAGATGAT
GAATTCATCAAAACTGGAAAATACTGATTCCTTGGATGCCTTAGTCCTTAGAGCCTAGATAATAAAGAGATGAAAGGGAA
TAAAATCACTTGTCAAGGTCTGGTGGATACTTCAAGATTTATATAAAAATCTATTAAGGTGAAGAATTACCATATCCCAA
TCCATGTACAGGCCACAGCAGAAGGTAACAATTTAGTGGCCACAAAAACTGTTAAAGACATGTGTAATAAAAAGATGAAA
AAAATCTGTGGTTGTAACAAGCCACTGCTAGTCCCAAATGCCTTGGAGGCCAAATAGCTGGAGCTTAAGGAAGAATCTGT
AAAGCTATTCTGAGAGGTGGCAGAGATGTGTGGGTAAAATTTTGGCTAGTGTTATCAGCAGCAGTTGGGGAGTAAAATAG
ATGAACAGTACATCTAGGATATCAAACACAATAATAGCAAAAATATCTTCCATGCAGTTTATACCCCTGCCACACTATTT
GTTCTTATCTTTATCACATAAGTGATTGCTGGTGTAACTAGATTCATTGGTTTGGACATGATAACTTGACTATGCAATAT
GATAATGGAATTGACCCTTATCACCCTGTGCCCCTGGACATACATTTGGTACTCTGGAGAATACGAAGAGCTGGATGCTG
TAATAGATCAGGTAGGTGCAGCCTTTTGAGACTCAGCCTTTTTACAAGCTTTA

Alignment

ORF - retro_amel_1328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.38 %
• Parental protein coverage: 65.89 %
• Number of stop codons detected: 13
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LRDSATVFALSTMISSIQVYNLSQ-NVQEDDLQHLQLFTEYGRLA-MEEIFLKPFQSLIFLVRDWSFPYE
          LRD.AT.F.L..MIS.I.VY.LSQ.NVQEDDLQ.LQLF.EYG.LA..E..FLKPFQSL.F.....S.P.E
Retrocopy LRDLATIFVLGKMISLI*VYILSQ<NVQEDDLQNLQLFAEYGQLA<REATFLKPFQSLTFFIEN*SYPIE

Parental  FSYGAEGGSKFLEKRLKVSGNQHEELQNVRKHIHSCFTKISCFLLPHPGLKVATNPNFDGKLKEIDDEFI
          F...A.GG.KFL...LK.S.NQHEELQNV.KH...CFTKI.CFLLP..GLKV..N..FDGK.KEIDDEFI
Retrocopy FGE-ANGGTKFLGNFLKFSENQHEELQNV*KHSYFCFTKIYCFLLPGHGLKVVPNLHFDGKFKEIDDEFI

Parental  K-NLKILIPWL-LSPESLDIKEINGNKITCRGLVE-YFKAYIKIYQGEELPHP-KSM-LQATAEANNLAA
          K.N.KILIPW..LSP.SLD.KE..GNKITC.GLV..YFK.YIKIY.GEELP.P..SM..QATAE.NNL.A
Retrocopy K<NWKILIPWM>LSP*SLDNKEMKGNKITCQGLVD<YFKIYIKIY*GEELPYP<QSM<VQATAEGNNLVA

Parental  VATAKDTYNKKMEEVCGGDKPFLAPNDLQTKHLELKEESVKLFRGVKKMGGEEFSRRYLHQLESEIDELY
          ..T.KD..NKKM...CG..KP.L.PN.L..K.LELKEESVKLF..V..M.G..F...Y..QL.S.IDE.Y
Retrocopy TKTVKDMCNKKMKKICGCNKPLLVPNALEAK*LELKEESVKLF*EVAEMCG*NFG*CYQQQLGSKIDEQY

Parental  IQYIKHNDSKNIFHAARTPATLFVVIFITYVIAGVTGFIGLDIIASLCNMIMGLTLITLCTWAYIRYSGE
          I..IKHN.SKNIFHA..TPATLFV.IFIT.VIAGVT.FIGLD.I..LCNMIM.LTLITLC.W.YI.YSGE
Retrocopy I*DIKHNNSKNIFHAVYTPATLFVLIFIT*VIAGVTRFIGLDMIT*LCNMIMELTLITLCPWTYIWYSGE

Parental  YRELGAVIDQVAAALWDQVSILAL
          Y.EL.AVIDQV.AA..D.....AL
Retrocopy YEELDAVIDQVGAAF*DSAFLQAL

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_1328 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1328 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	ENSAMEG00000009965	1 retrocopy	retro_amel_1328 ,