RetrogeneDB ID: retro_lafr_715

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_32:27886912..27888136(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDM2
• Ensembl ID: ENSLAFG00000005885
• Aliases: None
• Description: None

Sequence

>retro_lafr_715
GAAAGCACCTCACAGACTCCAAAGCCATTACTTTTGAAGTCGTTAAAGCCTGTTTGTGCACAAAAAGACACTTACACTAT
GAAAGGGGTTATATTTTATCTTGGCCTGTATATTATGGGTAAACAGTTATAAGACAAGAAGCAACAACATACGGTATATT
GTTCAAATGATCTTCTAGGGAATTTGTTTGGGGAGCCAAGCTCCTCTGTGAAAGACGACAGGAAAATATATACAAAGATC
TACAGAAACTTGGTAGTAGCCAATCGGCAGGAACCATCAGATTCCGGCACATCTGTGAGCGAAAATAGGTACCATCTTAA
AGACGGGAGTGATCCAAAGGACTCTGTGCAAGAGTTACAGGAAGAGAAACCTTCATCTTCAAATTTGATTTCGAGACCAA
ATACCTCATCTAGAAGGGGAGCAATCAGTGAGCCAGAAGAAAATTCAGATGAACTAGCCAGTGAAGGACAAAGAAAGCAC
CACAGATCAGGTAGTGTTTCCCTTCGCTCTGATGAAGCATTGTGCTGTGTGTAATAAGGGAGATACGTTGTGAAAAGCAG
TAGCAGTGGGTAAACAGAAACCCCATCAAATCCGGATCTTGATGCTGGTGTAAATGAACATTCTGGTGATTGGTTGGGCC
ACGATTCAGTTTCAGATCAGTTTGGTGTAAAATTTGAAGCTGAATCTCTTGATTCAGAAGATTCTAACTGTAGCCAAGAA
GGACAAGAACTCTCAGATAAAGATGTTGAGATATATCCAGTTACTGTCTATCAGGCAGAGGAGAGTGATACAGATTCATT
TGAAGATGACCCTGAAATTTCCTTAGCTAACTATTGGAAGTGTACTTCATGCAATGAAATGAACCCTCCTCTCCCACTGC
AACGTAACAGATGTCAGGCACTTCGTGAGAATTGGCTTCCTGAAGATAAAAGGAAAGATGAAGAGAAGATGCCTGAGAGC
ACGAAACTAGAAAACACAACACAAGTAGAAGAGGGCTTTGATGCTCCTGGTTATAAAAAAGCAACAGTAAATGACTCCAA
AGAGTCATGTGTTGAGGGAAATGATGATAAAATAACACAAGCCACCCAGTCTCAAGAAAGTGAGGACTATTCTCAGCCAT
CAACTTCCAGTAGCACCACTTATAGCAGCCAAGATGTCAGCGTTTAAGAGAAACACAAGGCAAAGAAGAAAACGTGGAAT
CTAGATATTGCCCTATTGCCGCTG

Alignment

ORF - retro_lafr_715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.82 %
• Parental protein coverage: 83.13 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QETLVRPKPLLLKLLKSVGAQKDTYTMKEVIFYLGQYIMAKRLYDEKQQHMVYCSNDLLGDLFGEPSFSV
          ..T...PKPLLLK.LK.V.AQKDTYTMK.VIFYLG.YIM.K.L.D.KQQH.VYCSNDLLG.LFGEPS.SV
Retrocopy ESTSQTPKPLLLKSLKPVCAQKDTYTMKGVIFYLGLYIMGKQL*DKKQQHTVYCSNDLLGNLFGEPSSSV

Parental  KDHRKIYTMIYRNLVVVNQQEPLDSGTSVSENRRQLEDGKGQKDSVQELQEEKPSSSNLISRPTTSSRRR
          KD.RKIYT.IYRNLVV.N.QEP.DSGTSVSENR..L.DG...KDSVQELQEEKPSSSNLISRP.TSSRR.
Retrocopy KDDRKIYTKIYRNLVVANRQEPSDSGTSVSENRYHLKDGSDPKDSVQELQEEKPSSSNLISRPNTSSRRG

Parental  AISETEENSDELASEGQRKRHRSDSVSLSFDESVALCVIREICCERSSSSDSTETPSNPDLDAGVSEHSG
          AISE.EENSDELASEGQRK.HRS.SVSL..DE....CV........SSSS..TETPSNPDLDAGV.EHSG
Retrocopy AISEPEENSDELASEGQRKHHRSGSVSLRSDEALC-CV**GRYVVKSSSSG*TETPSNPDLDAGVNEHSG

Parental  DWLDQDSVSDQFSVEFEVESLDSEDYNLSEEGQELSDEDDEVYRVTVYQAEESDTDSFEDDPEISLADYW
          DWL..DSVSDQF.V.FE.ESLDSED.N.S.EGQELSD.D.E.Y.VTVYQAEESDTDSFEDDPEISLA.YW
Retrocopy DWLGHDSVSDQFGVKFEAESLDSEDSNCSQEGQELSDKDVEIYPVTVYQAEESDTDSFEDDPEISLANYW

Parental  KCTSCNEMNPPLPPHCNRCWTLRENWLPEDKRKDKEKMPESAKQENTTQVEEGFDVPDCKKTTMNDSKES
          KCTSCNEMNPPLP...NRC..LRENWLPEDKRKD.EKMPES.K.ENTTQVEEGFD.P..KK.T.NDSKES
Retrocopy KCTSCNEMNPPLPLQRNRCQALRENWLPEDKRKDEEKMPESTKLENTTQVEEGFDAPGYKKATVNDSKES

Parental  CVEENDDKIKQASHSQEGEDYSQPSTSSSIIYSSQDARESEREETQGKDESVESRYRPI
          CVE.NDDKI.QA..SQE.EDYSQPSTSSS..YSSQD....E......K.........P.
Retrocopy CVEGNDDKITQATQSQESEDYSQPSTSSSTTYSSQDVSV*EKHKAKKKTWNLDIALLPL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_715 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004323	1 retrocopy	retro_cpor_1234,
Loxodonta africana	ENSLAFG00000005885	1 retrocopy	retro_lafr_715 ,
Otolemur garnettii	ENSOGAG00000034779	2 retrocopies	retro_ogar_1210, retro_ogar_49,
Ochotona princeps	ENSOPRG00000009677	1 retrocopy	retro_opri_891,
Ictidomys tridecemlineatus	ENSSTOG00000014702	1 retrocopy	retro_itri_1731,
Tupaia belangeri	ENSTBEG00000013758	2 retrocopies	retro_tbel_3216, retro_tbel_915,
Tarsius syrichta	ENSTSYG00000002908	2 retrocopies	retro_tsyr_1343, retro_tsyr_984,