RetrogeneDB ID: retro_amel_1730

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194114.1:190810..191588(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDM4
• Ensembl ID: ENSAMEG00000001126
• Aliases: None
• Description: Mdm4 p53 binding protein homolog (mouse) [Source:HGNC Symbol;Acc:6974]

Sequence

>retro_amel_1730
GGTCCTGCCACTGTTTTGGGTACTTGGCATGATGTGTGGGTTTTAAACGAGTTGGTATTAGAGTAGTTAGGTGCTGGGAC
AAAAGGAGAAGCTGTGAATACTGATCAAACAAGTAAAAAAAATCAGGAACTAAGTGACCAAAAGGTGACTGAAGTGGAAA
ACAAGGACCTTGAGGACTGTATACCCTGAAGTAATGACACTGGTGGAGAAGCCACTTCTGAGGATGAGTGGTAGTGTTAC
TGAGTGCAAGAAAATGAACTCTCCAAACCAGAGGTATTGCTGTTGCTGGGCCCTGAAGGATTAGTACTCAGACTGTTCTA
AGTGAGCCCATCGTCCCTTCGTTCCTGTGATCATTGCCACACCGGCAAAGAGGAAAATGAAGTAACTGATGTCCCTCCCT
GCCAAGGTGCCATTTTGGCTCCAGTCATTACAGCTGACCTATGAGAAAAGGAAGAAAAACCCAAATTTCCTGATTCCTGC
AGCTCAGTGGAATTCTCAGATTTGGCTCCTGGTTCTGAAAGCCCAGAGACCATCTCGAGCAAAATGGAACAATCAGATGG
CCTTACAGAGCAGAGACCAGATACACAAAATACGAAGGACTGACAAAAATTTCTTGACGCTGTATAGCACATGTGACAAG
TGGCTACAAGACAGAAATATTCCCGGAAGAACAGGCTACCCCATCACTTGTCTCCACTGCGCCAGAAGATTAAAGAAGCC
GGGGGCTTCACGCCCTCTTTGCAAGAACATTCAGTTGGTTATTAAGGTTTTTATGGCC

Alignment

ORF - retro_amel_1730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.76 %
• Parental protein coverage: 54.07 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GTAIVSDTTDDLWFLNESVSEQFGVGIKVEAADTERTSEEVGKVRDKKVTEVGKNDDLEDSKSLSDDTDV
          G.A.V..T..D.W.LNE.V.E..G.G.K.EA..T..TS.......D.KVTEV..N.DLED....S.DT..
Retrocopy GPATVLGTWHDVWVLNELVLE*LGAGTKGEAVNTDQTSXXXQELSDQKVTEV-ENKDLEDCIP*SNDTGG

Parental  EVTSEDEWQC-TECKKFNSPSKRYCFRCWALRKDWYSDCSKLTHSLSTSDITAIPEKK-ENEGIDVPDCR
          E.TSEDEW.C.TECKK.NSP..RYC..CWAL.KD.YSDCSK..H......I.A.P.K..ENE..DVP.C.
Retrocopy EATSEDEW*C>TECKKMNSPNQRYCC-CWAL-KD*YSDCSK*AHRPFVPVIIATPAKR<ENEVTDVPPCQ

Parental  RTISAPVVRPKGEYTKEEKNPKLFDPCNSVEFLDLAHSSESQETISSMGEQSDNLFEQRTDTENMEDCQ-
          ..I.APV..........E..PK..D.C.SVEF.DLA..SES.ETISS..EQSD.L.EQR.DT.N..D.Q.
Retrocopy GAILAPVIT--ADL*EKEEKPKFPDSCSSVEFSDLAPGSESPETISSKMEQSDGLTEQRPDTQNTKD*Q>

Parental  NLLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKVFIA
          N.L...S.C.K...D.NI..GRTG...TC.HCARRLKK.GAS.P.C.K.IQLVIKVF.A
Retrocopy NFLTLYSTCDKWLQDRNI-PGRTGYPITCLHCARRLKKPGASRPLC-KNIQLVIKVFMA

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_1730 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1730 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001126	1 retrocopy	retro_amel_1730 ,
Macaca mulatta	ENSMMUG00000011236	1 retrocopy	retro_mmul_2475,
Mus musculus	ENSMUSG00000054387	1 retrocopy	retro_mmus_3520,
Otolemur garnettii	ENSOGAG00000011679	1 retrocopy	retro_ogar_1852,
Ictidomys tridecemlineatus	ENSSTOG00000004184	1 retrocopy	retro_itri_428,