RetrogeneDB ID: retro_amel_1552

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193606.1:60368..60764(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS19BP1
• Ensembl ID: ENSAMEG00000010936
• Aliases: None
• Description: ribosomal protein S19 binding protein 1 [Source:HGNC Symbol;Acc:28749]

Sequence

>retro_amel_1552
GCCTTGCTGCAGCAGGACTGGGAGCTGCGGGGGGCAGTCGAGGCCCCGGAACCAGGCAAGGCCAAGCCCAGCAGGGCTCT
GGTAAAGCGCACCAGGAAAACAAATGCAACCCAAGCCCAGAAACGACAGAACTCAGCCAAGGGAAAGGTGCCCAAGTCGG
TACTTGCTGAGTTCCTGAAGTGAGAGCATCAAGTCTACCTGAGAGTCAACCTGAAGTTTATGACCAGTGTGAGAAGCACA
GTGGCTGAGTTGGTCACCTAGCCGATTGCATGCCAGAACTGGGGCCACAAGGCCTGTGACCAGCCTATGGCCAAGATGAA
GAAGTAGACGGCAGCTGAGAGCACCCTGTTTACAGAGGAAGACTTCCAGAAGTTCCATCAGGAGTACTTCAGCAGC

Alignment

ORF - retro_amel_1552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.91 %
• Parental protein coverage: 97.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALLRRGLELLGAPEAPRAAPGQAKPSGAPAKRTRKAKATQAQKLRNSAKGKVPKDALAEFQKREHRGYLG
          ALL....EL.GA.EAP...PG.AKPS.A..KRTRK..ATQAQK..NSAKGKVPK..LAEF.K.EH..YL.
Retrocopy ALLQQDWELRGAVEAPE--PGKAKPSRALVKRTRKTNATQAQKRQNSAKGKVPKSVLAEFLK*EHQVYLR

Parental  VNLKFMTSARTTVAESVTRQIVRQNRGRKACDRPVAKTKK-KKAEGTVFTEEDFQKFQQEYFGS
          VNLKFMTS.R.TVAE.VT..I..QN.G.KACD.P.AK.KK...AE.T.FTEEDFQKF.QEYF.S
Retrocopy VNLKFMTSVRSTVAELVT*PIACQNWGHKACDQPMAKMKK*TAAESTLFTEEDFQKFHQEYFSS

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_1552 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1552 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	ENSAMEG00000010936	1 retrocopy	retro_amel_1552 ,
Erinaceus europaeus	ENSEEUG00000009817	1 retrocopy	retro_eeur_3,
Felis catus	ENSFCAG00000029275	1 retrocopy	retro_fcat_1374,