RetrogeneDB ID: retro_amel_1630

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193800.1:32005..32838(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP5
• Ensembl ID: ENSAMEG00000015745
• Aliases: None
• Description: dual specificity phosphatase 5 [Source:HGNC Symbol;Acc:3071]

Sequence

>retro_amel_1630
GTCCGGCGCTCCTTGCTTCTCGCCTGCCCTTCTGCGCTCGCGGGTCTACTTCCTCAAAAGGAGTAGGAAAGGAGGTAGGA
GGGTTTCTATTCAGAATATCCTGAGTGTTGCATGGATGGAAAACCGATTTCACAAGAGAAGGTTAAAACCAAGAAACCTC
TCGTGAGCCAGTGTGGGAAACCAGTGCTCAACATCACCTACAGGCCAGCTTATGACCAGGGCGGCCCAGTTGAAGTCCTT
CTGTTGCTCCACTTTGGAGGAGACCACTGTGCATCCAAGTGCGAGTTCTTGGCCAACCGCTACATCACAGCCCTGCTGAA
TGTCTCACAGCAGAACTTGGAATCCTGCATGACCCACCTGCAGTACAAATGTAACCCGTGTAAGACAATCACATGGCTGA
CATTAGCTCCTACTTTCAATAACCAATAGGCTTCACGGACTATGTCAGAGAAAGGGGAAGCAAGATCCTGGTTCACTGTG
AGGCTGGGCTCTCCCATTCACACACCATCTGCATGGCTTACCTAATGAAGAGCAAGCAGTTCTGCCTGAAGGATGCCTTC
GATTACATCAAGCAGACGAGGAACGTGGGCTTCCCCAACTTTGGCTTCGTAGACCAGCAGCTCCTGCGGTATGTGTCTGA
GATCCTGCCTTCCACACCAACCCCCCAGGCTCCCTCCTGCCAAGGAGAGGCAGCCAGCTCTTCATTGCAGACACTGAGCC
CTAATATCCAGGATTTCTACTGCATATTCTCTACCTCAGTGCTGGTTCCAGTGCCTACCCATTCAACAGTCTCAGAGCTC
AGCAGGAGCCCCACGGCCACAACCACATCCTGC

Alignment

ORF - retro_amel_1630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 94.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLTSLLACLPAG-PRVYFL----KGGY-ETFYSEYPECCVDVQPISQEKVEAEKALVSQCGKPVLSVSYG
          V..SLL...P....RVYFL....KGG..E.FYSEYPECC.D..PISQEKV...K.LVSQCGKPVL...Y.
Retrocopy VRRSLLLACPSA>SRVYFLKRSRKGGR<EGFYSEYPECCMDGKPISQEKVKTKKPLVSQCGKPVLNITYR

Parental  PAYDQGGPVEILPFLYLGSAYHASKCEFLANLHITALLNVSRRISESCPTHLHYK-WLPVEDSHTADISS
          PAYDQGGPVE.L..L..G....ASKCEFLAN..ITALLNVS....ESC.THL.YK...PV.D.H.ADISS
Retrocopy PAYDQGGPVEVLLLLHFGGDHCASKCEFLANRYITALLNVSQQNLESCMTHLQYK<M*PV*DNHMADISS

Parental  HFQEAIDFIDCVREKGGKVLVHCEAGISRSPTICMAYLMKAKQFRLKDAFDYIKQRRGVVSPNFGFMG-Q
          .FQ..I.F.D.VRE.G.K.LVHCEAG.S.S.TICMAYLMK.KQF.LKDAFDYIKQ.R.V..PNFGF...Q
Retrocopy YFQ*PIGFTDYVRERGSKILVHCEAGLSHSHTICMAYLMKSKQFCLKDAFDYIKQTRNVGFPNFGFVDQQ

Parental  LLQYESAILPS--TPQAPSCQGEAASSSFIAHLQTLSPDLQGSYCTFPTSVLAPVPTHSTVSELGRSPMA
          LL.Y.S.ILPS..TPQAPSCQGEAASSS....LQTLSP..Q..YC.F.TSVL.PVPTHSTVSEL.RSP.A
Retrocopy LLRYVSEILPSTPTPQAPSCQGEAASSS----LQTLSPNIQDFYCIFSTSVLVPVPTHSTVSELSRSPTA

Parental  TATSC
          T.TSC
Retrocopy TTTSC

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_1630 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1630 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015745	1 retrocopy	retro_amel_1630 ,
Dasypus novemcinctus	ENSDNOG00000001858	1 retrocopy	retro_dnov_1665,
Equus caballus	ENSECAG00000013514	2 retrocopies	retro_ecab_188, retro_ecab_612,