RetrogeneDB ID: retro_amel_1224

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193066.1:9707..10383(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TWF1
• Ensembl ID: ENSAMEG00000017332
• Aliases: None
• Description: twinfilin actin-binding protein 1 [Source:HGNC Symbol;Acc:9620]

Sequence

>retro_amel_1224
AGTGTAGGTGTTAAAGATGCCTTTGCCAGAGCAAGCAAAGGAAAATAACGACTTCTACAACTCTCTATTGAAAATGAGAA
ACTTGGGACTGGATCCTGTAGTCAGCCTTCAGATTGCTGGGGTAAGGACTGCGATTCCCTTGGTTTACCCCTCCTGTAGG
ACAGACAACCGTGCTGGATAGTACTCAGGTTAGACTCTCAGAATGCCCAGGGATACGAATGCATAGTCATTGTCTGCTCT
CCAGAACATTCTCGTGTTCGTCAAATAATGTTGTGTGCAGCAACGAGAGCGACTCTGAAAAAGGAGTTCGGAGGCGGCAC
ATTGAAGATGAAGTGTTTGGACAGTAAGGGAAGATGCATCATTACATGGACATGAAAACACGTGCAGTCACATCTTCTCC
TGCACCGATGACTCCAGCTGAGGAAGAATTACGGCAGATTAAAGGTAAGGAGGTACAAACTGACGTGGGTGTGGACACGA
AGCATCAAACACTACAAGGAGTAGGATTTCCTACTCGTCGAGAGGCTTTTCAGGCTTTGGAAAAATTAAGTAACAGAAGC
TCAACTCTGTGCAGTTGGAAATAGATATGAAAAATGAAATTACAATTTCAGACAACACAACAAACACAGAACTAAAAGAT
TTGCCAAGGAGGATTCCCAAGGATTCAGCACACTAC

Alignment

ORF - retro_amel_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.71 %
• Parental protein coverage: 65.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SEDVKDIFARARNGKYRLLKISIENEKLVIGSCSQPSGSWDKDYDSFVLPLLEDKQPCYILFRLDSQNAQ
          S..VKD.FARA..GK.RLL..SIENEKL..GSCSQPS..W.KD.DS..LPLL.D.QPC.I..RLDSQNAQ
Retrocopy SVGVKDAFARASKGK*RLLQLSIENEKLGTGSCSQPSDCWGKDCDSLGLPLL*DRQPCWIVLRLDSQNAQ

Parental  GYEWIFIAWSPDHSHVRQKMLYAATRATLKKEFGGG-HIKDEVFG-TVKEDVSLHGYK-KYLVSQ-SSPA
          GYE.I.I..SP.HS.VRQ.ML.AATRATLKKEFGGG.HI.DEVFG.TV.ED.SLHG...K...S..SSPA
Retrocopy GYECIVIVCSPEHSRVRQIMLCAATRATLKKEFGGG<HIEDEVFG<TVREDASLHGHE<KHVQSH<SSPA

Parental  PLTAAEEELRQIKINEVQTDVGVDTKHQTLQGVAFPISREALQALEQLSNR-QLNYVQLEIDIKNEIIIL
          P.T.AEEELRQIK..EVQTDVGVDTKHQTLQGV.FP..REA.QALE.LSNR..LN.VQLEID.KNEI.I.
Retrocopy PMTPAEEELRQIKGKEVQTDVGVDTKHQTLQGVGFPTRREAFQALEKLSNR<KLNSVQLEIDMKNEITIS

Parental  ASTTNTELKDLPKRIPKDSARY
          ..TTNTELKDLP.RIPKDSA.Y
Retrocopy DNTTNTELKDLPRRIPKDSAHY

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_1224 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1224 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017332	1 retrocopy	retro_amel_1224 ,
Choloepus hoffmanni	ENSCHOG00000008386	5 retrocopies	retro_chof_1525, retro_chof_2013, retro_chof_2569, retro_chof_391, retro_chof_509,
Homo sapiens	ENSG00000151239	2 retrocopies	retro_hsap_1819, retro_hsap_4916,
Monodelphis domestica	ENSMODG00000018535	1 retrocopy	retro_mdom_167,
Mustela putorius furo	ENSMPUG00000000364	1 retrocopy	retro_mputfur_1629,
Mus musculus	ENSMUSG00000022451	1 retrocopy	retro_mmus_2961,
Nomascus leucogenys	ENSNLEG00000017931	1 retrocopy	retro_nleu_2877,
Otolemur garnettii	ENSOGAG00000007525	1 retrocopy	retro_ogar_1058,
Pan troglodytes	ENSPTRG00000004846	1 retrocopy	retro_ptro_3279,
Rattus norvegicus	ENSRNOG00000022507	1 retrocopy	retro_rnor_2176,