RetrogeneDB ID: retro_amel_934

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192756.1:666734..667118(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R14B
• Ensembl ID: ENSAMEG00000018019
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14B [Source:HGNC Symbol;Acc:9057]

Sequence

>retro_amel_934
CCTGAGCCAGGCATTGGTGACCCAGGGCCCAATGTCTACCTTCAGGGCACACCTGGGGTGCAGGTGAGGGCCCCAGGCTG
CGGACCAGGAGAGCCCAGTGAGGCACCAAGGGAAGGTCACTGTCAAATAAGGCCACAAGGAGCAAGGGAAGCACTTCAAC
CTGGAGGAGTGAATTCAGGGGAAGCTTACTTGCTTCTACGACTTCCAGGAAGAGATCCCAGAATTGGAGATTGATGTGGA
TGAACTCTTGGATGTGGAGAGTGATGATACCAGGGCTGTTGGGGTCAAGGAGCTGCTGGGTGACTGTTACAAACCCACTG
GGGCCTTCTCTGGCTGGCTGGACAAGACCTGGAGCATGTGGAACTGAGCACACCCCAAAAGAAG

Alignment

ORF - retro_amel_934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.91 %
• Parental protein coverage: 88.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PGPGSGGPGPRVYFQSPPGA-AGEGPG-GADDEGPVRRQGKVTVKYDRKELRKRLNLEEWILEQLTRLYD
          P.PG.G.PGP.VY.Q..PG..AGEGP...AD.E.PVR.QGKVTVK...KE..K..NLEE.I...LT..YD
Retrocopy PEPGIGDPGPNVYLQGTPGV<AGEGPR<AADQESPVRHQGKVTVK*GHKEQGKHFNLEE*IQGKLTCFYD

Parental  CQEEEIPELEIDVDELLDMESDDTRAARVKELLVDCYKPTEAFISGLLDKIRGM-QKLSTPQKK
          .Q.EEIPELEIDVDELLD.ESDDTRA..VKELL.DCYKPT.AF.SG.LDK...M...LSTPQKK
Retrocopy FQ-EEIPELEIDVDELLDVESDDTRAVGVKELLGDCYKPTGAF-SGWLDKTWSM<VELSTPQKK

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_934 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_934 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018019	1 retrocopy	retro_amel_934 ,
Felis catus	ENSFCAG00000030667	1 retrocopy	retro_fcat_1417,
Mus musculus	ENSMUSG00000056612	5 retrocopies	retro_mmus_1045, retro_mmus_2245, retro_mmus_2624, retro_mmus_30, retro_mmus_3473,
Otolemur garnettii	ENSOGAG00000030926	2 retrocopies	retro_ogar_3158, retro_ogar_376,
Pteropus vampyrus	ENSPVAG00000017120	1 retrocopy	retro_pvam_1095,
Rattus norvegicus	ENSRNOG00000021151	2 retrocopies	retro_rnor_1262, retro_rnor_41,