RetrogeneDB ID: retro_amel_607

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192524.1:1692287..1692978(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000000826
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSPH
• Ensembl ID: ENSAMEG00000016118
• Aliases: None
• Description: phosphoserine phosphatase [Source:HGNC Symbol;Acc:9577]

Sequence

>retro_amel_607
AGAAAAATTCTTTCAAGAATGGTCTCCCATTCAGAGTTGCGGAAGCTTTTCTGTTCAGCTGTGCAGTACGCTTTGATGTG
GGTAGCACAATCATCAGAGACGATGGAATTGGTAAGCTAGCCAAGTTCTGTGGAGTTGAGGATGCTCTGTCAGAACTGAC
ACAGCGAGCCGTGGGTGGGGCAGTGCCTTTCATGGCTGCCCTCACAGAGCACTTAGCCCTCATCCAGCCCTCCCGGGGAG
CAGATGTGAAGGCTCATAGTAGAGCACCCCCTACACCTGACCCGGGGCATAAGGGAGGTAGTAAGCCGCCTGCAAGAGCG
AAATGTTCAGGCTTCCCTCTTATCCGGTGACCTTAGGAGCTTTGTAGAGCACGTTGCTTCAGAGCTCAGTATCCCATCAA
CCAACACATTTGCCAGTAGCTGAAATTCTACTTCGATGTGAATATGCAAGTGTTGATGAAATGCAGCCAACAGCCAATTC
TGGTGGGGAAGGAAAGGTTCTTAAACTTGTGAAGGAAAAATTTCATTTTAAGTCAATAGTTATGATTAGTCATGGAGACA
TAGACATGGAAACCTGTCCTCCTGCTGATGTTCCCATTGGATTTGGAGGAAATGTGATCAGACAACAAGTAAAAAACAAC
TTGGAATGGTACATCACTGACATTGTAGAGATTTTGGGAGAACTTAAAAAA

Alignment

ORF - retro_amel_607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RKSLPRMVSHSELRKLFCSAD-AVCFDVDSTVIREEGIDELAKFCGVEDAVSEMTRRAMGGAVPFKAALT
          RK.L.RMVSHSELRKLFCSA..AV.FDV.ST.IR..GI..LAKFCGVEDA.SE.T.RA.GGAVPF.AALT
Retrocopy RKILSRMVSHSELRKLFCSAV<AVRFDVGSTIIRDDGIGKLAKFCGVEDALSELTQRAVGGAVPFMAALT

Parental  ERLALIQPSR-EQVQRLIAEHPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPPTNVFA
          E.LALIQPSR.EQ..RLI.EHP.HLT.GIRE.VSRLQERNVQ..L.SG..RS.VEHVAS.L.IP.TN.FA
Retrocopy EHLALIQPSR>EQM*RLIVEHPLHLTRGIREVVSRLQERNVQASLLSGDLRSFVEHVASELSIPSTNTFA

Parental  NR-LKFYFNG-EYAGFDEMQPTAESGGKGKVIKLLKEKFQFKKIVMIGDGATDMEACPPADVFIGFGGNV
          ...LKFYF...EYA..DEMQPTA.SGG.GKV.KL.KEKF.FK.IVMI..G..DME.CPPADV.IGFGGNV
Retrocopy SS<LKFYFDV<EYASVDEMQPTANSGGEGKVLKLVKEKFHFKSIVMISHGDIDMETCPPADVPIGFGGNV

Parental  IRQQVKDNAEWYITDFVELLGELEE
          IRQQVK.N.EWYITD.VE.LGEL..
Retrocopy IRQQVKNNLEWYITDIVEILGELKK

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_607 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_607 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	ENSAMEG00000016118	1 retrocopy	retro_amel_607 ,
Felis catus	ENSFCAG00000021883	1 retrocopy	retro_fcat_183,
Ictidomys tridecemlineatus	ENSSTOG00000026898	1 retrocopy	retro_itri_1159,