RetrogeneDB ID: retro_lafr_489

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_19:37604273..37605225(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR73
• Ensembl ID: ENSLAFG00000010104
• Aliases: None
• Description: None

Sequence

>retro_lafr_489
TTGATATTACCTCTCAGACTTTCCGGGAAGAGAACTAGGACTCATTCCCAGAAAGAGATTTCAAGGCGCACCACGGAGGA
TTTTCAGACAAATCTGTCTTTCATCTAAAGCACGTGCCAGAAACCAGGTTGCTGGTGACCTGTGGCCTTTCAGGTGTTTC
CCTACAGGTGTGGCTGATTGCAGAGGAAGTGATGTCATTAAAGCTGTCAGCTCCATTGCTGTGCATGAGGAGAAGGCGAG
TCCCTGGCCCAGGATGTCTGTCTTCTCCTCCATGGCCCCTGGAGTCCTCCACAGGGCGCGGCTTAGCAGTCTGAGGATTC
CAGACCTGGAATCCCAGAAGACCAGGTAAACTGCAGGTGTTAGTGACAGTGGGGTTCTCTGTAGGCTGCAGGTCCTGGGT
ATAAACACCTTTGCTTTCTGCTGTACCTCACGCTGGCTGGGGCTTGTTGACATCCGCCAGAAATGGGCACCTTCTGAGAA
CCTCAGCCCTGGCCCTGGGTCTGGCGGAGGGAGGTGGTGTGCAGAAGTTGAGGACAGTGGCCAGCGCCCTGGGCCCAGCA
TTGCCAGCCTTGGCTCAAACAGACAACTCTGTCTCCTCAACCCCCGGTGATCTCTGCTACCCTGTGAGTTCAGCCCAGTG
CCCATTGTCCATGCCTAGCCCTGACCCAGAGTTGCTGCGAGTAACTTGGGCCCTGGTCCTGGAAACTGCCTAGCCATTTC
AGGTTTTCATGGGACAAACCAGGTTTATGATGTCACATCTTGGGGTAGAGTGGAGAGCCAAGCAGAATCTCTCTTCTTTC
ACAGAGGTTACATTTTCCAATATGCAAATGAACTGGACACTACTCCACTGGTCACCTTCCACATCTGGCACCCCTGGAAA
CCAAGGACTTTATTATCTGCACCAAATGATGCCTCTCTGCATGCGCGGAACTGGGTGGAACTTCATGCTTCC

Alignment

ORF - retro_lafr_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.16 %
• Parental protein coverage: 85.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LILPLRLSVK-ENQGLFPERDFKVCHGGFSDKPVFDLKHVPETRLLLTSGLPGCSLQVWQIAED-SDVIK
          LILPLRLS.K.EN...FPERDFK..HGGFSDK.VF.LKHVPETRLL.T.GL.G.SLQVW.IAE..SDVIK
Retrocopy LILPLRLSGK<EN*DSFPERDFKAHHGGFSDKSVFHLKHVPETRLLVTCGLSGVSLQVWLIAEE<SDVIK

Parental  AVSTIAMHEEEESLWPRMAVFSSVAPGVLHGARLSSLKITDLESQKIMYASGVGDREALSSLQVLGADTF
          AVS.IA.HEE..S.WPRM.VFSS.APGVLH.ARLSSL.I.DLESQK.....GV.D...L..LQVLG..TF
Retrocopy AVSSIAVHEEKASPWPRMSVFSSMAPGVLHRARLSSLRIPDLESQKTR*TAGVSDSGVLCRLQVLGINTF

Parental  AFCCTSGRLGLVDIRQKWAPSE--SPGPGSGGGRWCAEVRSRDQDPGPSIASLGSNGQLCLLDPR-DLCH
          AFCCTS..LGLVDIRQKWAPSE..SPGPGSGGGRWCAEV....Q.PGPSIASLGSN.QLCLL.PR.DLC.
Retrocopy AFCCTSRWLGLVDIRQKWAPSENLSPGPGSGGGRWCAEVEDSGQRPGPSIASLGSNRQLCLLNPR>DLCY

Parental  PVSSVQCPVSRPSPDPELLQVTWAPVLD-NCLAISGFDGTVQVYDVTSWGGIESQVEPLFTHRGHIFLDA
          PVSS.QCP.S.PSPDPELL.VTWA.VL..NCLAISGF.GT.QVYDVTSWG..ESQ.E.LF.HRG.IF..A
Retrocopy PVSSAQCPLSMPSPDPELLRVTWALVLE<NCLAISGFHGTNQVYDVTSWGRVESQAESLFFHRGYIFQYA

Parental  NELDAAPLVTTHIWHPCKPRTLLSAADDASLHVWDWVDLCAS
          NELD..PLVT.HIWHP.KPRTLLSA..DASLH...WV.L.AS
Retrocopy NELDTTPLVTFHIWHPWKPRTLLSAPNDASLHARNWVELHAS

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_489 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000010104	1 retrocopy	retro_lafr_489 ,
Tarsius syrichta	ENSTSYG00000006739	1 retrocopy	retro_tsyr_1995,