RetrogeneDB ID: retro_amel_619

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192530.1:1070575..1071190(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB3
• Ensembl ID: ENSAMEG00000004363
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 3 [Source:HGNC Symbol;Acc:9540]

Sequence

>retro_amel_619
AGGTCTATTATGTCCTCTAATGGAGGGGCCATCATGGCCATGAATGGGAAGAACTGTGTGGCCATTGCTGCCAAAAGGTG
CTTTGGCATCCAATCTCAGATGGTGACCATGGACTTCCAGAAGATCTTTCCTGTGGGCAATTGGCTGTACATAGGCCTGG
CTGGGCTCACCACTGATTTCCAGACTGTTGCTCAGCACCTCAAGTTCTAGCTGAACCTCTATGAGCTGAAGGAAGGTTGG
CAGGTCAAGCCTCATACCCTCATGAGCATGGTGGCCAACGTCTTGTATGAAAAATGGTTTGGCCCCTACTACACAGAGCC
AGTCATCACTGGGTTGGACCTGAAGACCCTTAAGTCCCTCATTTGCTCTCTAGACCTTATCTGCTGCCCCATGGTGACGG
ACAACTTTGTGGTCAGTAGCACCTGCTCCAAACAATATATGGGGTGTGTGAGTCCCTCTGGGGGCCTGACGTAGATCCAG
AACAGAAGTTTGAAACCATCTCGCAAACCATGCTGAATGCTGTGGATCAGGATGTACCGTTCAGGCATGGGAGTCATTGT
CCACATCACTGAGAAGAACAAAATTACCACCGGGACACTGAGGGCCTGAATGGAC

Alignment

ORF - retro_amel_619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFR
          .SIMS.NGGA.MAM.GKNCVAIAA.R.FGIQ.QMVT.DFQKIFP.G..LYIGLAGL.TD.QTVAQ.LKF.
Retrocopy RSIMSSNGGAIMAMNGKNCVAIAAKRCFGIQSQMVTMDFQKIFPVGNWLYIGLAGLTTDFQTVAQHLKF*

Parental  LNLYELKEGRQIKPYTLMSMVANLLYERRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSG
          LNLYELKEG.Q.KP.TLMSMVAN.LYE..FGPYYTEPVI.GLD.KT.K..ICSLDLI.CPMVTD.FVVS.
Retrocopy LNLYELKEGWQVKPHTLMSMVANVLYEKWFGPYYTEPVITGLDLKTLKSLICSLDLICCPMVTDNFVVSS

Parental  TCSEQ-MYGMCESLWEPNMDPEHLFETISQAMLNAVDRDAV-SGMGVIVHIIEKDKITTRTLKARMD
          TCS.Q..YG.CESLW.P..DPE..FETISQ.MLNAVD.D...SGMGVIVHI.EK.KITT.TL.A.MD
Retrocopy TCSKQ<IYGVCESLWGPDVDPEQKFETISQTMLNAVDQDVP>SGMGVIVHITEKNKITTGTLRA*MD

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_619 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_619 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 12 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004363	1 retrocopy	retro_amel_619 ,
Canis familiaris	ENSCAFG00000016587	2 retrocopies	retro_cfam_135, retro_cfam_532,
Erinaceus europaeus	ENSEEUG00000015275	1 retrocopy	retro_eeur_10,
Felis catus	ENSFCAG00000014497	3 retrocopies	retro_fcat_1270, retro_fcat_1442, retro_fcat_784,
Gorilla gorilla	ENSGGOG00000007067	2 retrocopies	retro_ggor_103, retro_ggor_876,
Loxodonta africana	ENSLAFG00000002233	1 retrocopy	retro_lafr_70,
Macropus eugenii	ENSMEUG00000004131	2 retrocopies	retro_meug_1804, retro_meug_551,
Macaca mulatta	ENSMMUG00000012363	1 retrocopy	retro_mmul_868,
Monodelphis domestica	ENSMODG00000012614	2 retrocopies	retro_mdom_1722, retro_mdom_1812,
Mus musculus	ENSMUSG00000069744	8 retrocopies	retro_mmus_1449, retro_mmus_1551, retro_mmus_1790, retro_mmus_1938, retro_mmus_2110, retro_mmus_41, retro_mmus_46, retro_mmus_536,
Rattus norvegicus	ENSRNOG00000012938	7 retrocopies	retro_rnor_1016, retro_rnor_2094, retro_rnor_2448, retro_rnor_2537, retro_rnor_2804, retro_rnor_743, retro_rnor_8,
Tupaia belangeri	ENSTBEG00000013010	2 retrocopies	retro_tbel_1387, retro_tbel_2693,