RetrogeneDB ID: retro_lafr_980

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_56:2865876..2867104(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSLAFG00000012217
• Aliases: None
• Description: None

Sequence

>retro_lafr_980
AAGGACTTGCTAGTGCAGTATGCCACAGGAAAGAAAAGCTTCAAACACAAGAAAAAGTTGGAAAAGGCTATGAATGTCCT
GAGGAAACAAAAGAAGAAAAACAAAAAAACAAGAGTGTTTAATTTTTCAGCTATTCACTTGATTCATGATCCCCAAGATT
TTGCAGAAAAATTACTAAGGCAGCTATAGAGCTCTAAGGAAAGGCTTGAAGGGAAGATGTAGCTCATGAACCTTGTCTCC
AGATTGGTGGGAATTCATGAGCTTTTTCTCTTTGACTTCTATCTTCTTGTGCCAAGATTCCTGCAGTCCCACCAAACAGA
AGTAACAAAGATCCCTGTTTTCTGGATAAGCATCTTATCACCTGGTAGCTCCGGAATTTATTCAGCCATTGCTCATGACT
GTGGCCAACAATTTTGTTACCAATAAGAACCCTGACAAAGTCATGACAGTAGGAATCAATGCCATAAAAGAGATAACAGC
TCTATATCCTCTAGCCATGACTGAATAACTTCTCCAAGACCTAGCCCAGTAGAAAACATGCAAAGATAAGAATGTGATGA
TGTTCACTAGAGTTCTGATTCAGCTCTTCCAAACACTGACTCCTCAGATGTTACAAGGTAAGCCTATAGAGGCCTCAATA
GAAGCAAGAGTGCAAGAATATGGAGTATTAGATGGTAAAGGTTACATTCCAGGAGCAGAAATTCTGGATGTGGAAAAAGA
GGAAGAGAATGATGAAAATGGGTGGCAAAGTACCAGTCTCAGTGAGGAGGATGCCAATAGTGAATGAGTTGACCTGCACC
ATTCTGATAAAGAACAGCAAGAAATCTCCAAGAAGCTGAACAGCATGCCTGCGGAGGAGCAGAAAGCCAAAGCTGCAGCC
ATCAGTACTAGCCCAGTTTTGACCCAGGAAATCTTCCAAAAAATCCACATGGGCCAACTAAAAAAAGAACTCAGTGCTGC
TCCTGGGGAAAGCAGAGAAAAAAGGAAATATGGTGAAATAGAGAGCAAGAAGGAGCCCAGGGATGAGTTACTTTCACTTT
GGCACCTTGAAAGCATTCATAAAAAGCCGAAGTCTAACAAGGACATAAGTCTAGCAGCTGCAAATGCTGGAAAGGCAGAT
CAAAAAGAATTTGTGAGGAAGAAAAACAGAATGAATCCATTTTCCAGTCCCACAAATAAACAGAAAAAAAACCAAAAGAA
CTTAATGATGATACGGCATAGCCAGAAT

Alignment

ORF - retro_lafr_980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 60.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDLLVQYATGKKSSKHKKKLEKAMKVLKKQKKK-KKPEVFNFSAIHLIHDPQDFAEKLLKQLESSKERFE
          .DLLVQYATGKKS.KHKKKLEKAM.VL.KQKKK.KK..VFNFSAIHLIHDPQDFAEKLL.QL.SSKER.E
Retrocopy KDLLVQYATGKKSFKHKKKLEKAMNVLRKQKKKNKKTRVFNFSAIHLIHDPQDFAEKLLRQL*SSKERLE

Parental  VKMMLMNLTSRLVGIHQLFLFNFYPFIQRFLQPHQREVTKILLFAAQ-ASHHLVPPEIIQSLLMTVANNF
          .KM.LMNL.SRLVGIH.LFLF.FY....RFLQ.HQ.EVTKI..F......H...P.E.IQ.LLMTVANNF
Retrocopy GKM*LMNLVSRLVGIHELFLFDFYLLVPRFLQSHQTEVTKIPVFWIS>SYHLVAP-EFIQPLLMTVANNF

Parental  VTDKNSGEVMTVGINAIKEITTRCPLAMTEELLQDLAQYKTHKDKNVMMSARTLIQLFRTLNPQMLHKKF
          VT.KN...VMTVGINAIKEIT...PLAMTE.LLQDLAQ.KT.KDKNVMM..R.LIQLF.TL.PQML....
Retrocopy VTNKNPDKVMTVGINAIKEITALYPLAMTE*LLQDLAQ*KTCKDKNVMMFTRVLIQLFQTLTPQML----

Parental  RGKPTEASIEARVQEYGELDAKDYIPGAEVLEVEKEEENAENDEDGWESASLSEEEDADGEWVDVSHSSD
          .GKP.EASIEARVQEYG.LD.K.YIPGAE.L.VEKEEEN...DE.GW.S.SLS.EEDA..E.VD..H.SD
Retrocopy QGKPIEASIEARVQEYGVLDGKGYIPGAEILDVEKEEEN---DENGWQSTSLS-EEDANSE*VDL-HHSD

Parental  EEQQEISKKLNSMPMEERKAKAAAISTSRVLTQEDFQKIRMAQLRKELSAAPGKA-EKRKYIEIDSDEEP
          .EQQEISKKLNSMP.EE.KAKAAAISTS.VLTQE.FQKI.M.QL.KELSAAPG...EKRKY.EI.S..E.
Retrocopy KEQQEISKKLNSMPAEEQKAKAAAISTSPVLTQEIFQKIHMGQLKKELSAAPGESREKRKYGEIESKKE-

Parental  SPRGELLSLRDIERLHKKPKSDKETRLATAMAGKTDRKEFVRKKTKINPFSSSTNKEKKKQKNFMMMRYS
          .PR.ELLSL...E..HKKPKS.K...LA.A.AGK.D.KEFVRKK...NPFSS.TNK.KK.QKN.MM.R.S
Retrocopy -PRDELLSLWHLESIHKKPKSNKDISLAAANAGKADQKEFVRKKNRMNPFSSPTNKQKKNQKNLMMIRHS

Parental  QN
          QN
Retrocopy QN

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_980 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008521	2 retrocopies	retro_cfam_1211, retro_cfam_515,
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510, retro_cpor_994,
Echinops telfairi	ENSETEG00000004811	2 retrocopies	retro_etel_1946, retro_etel_779,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980 ,
Microcebus murinus	ENSMICG00000006682	1 retrocopy	retro_mmur_1204,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Sus scrofa	ENSSSCG00000008974	1 retrocopy	retro_sscr_571,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414,