RetrogeneDB ID: retro_lafr_641

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_28:5425711..5426768(+)
• Located in intron of: ENSLAFG00000002717

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35B3
• Ensembl ID: ENSLAFG00000002579
• Aliases: None
• Description: None

Sequence

>retro_lafr_641
ATGGATCTGAAGTTCAGCAGCTCCAGGAAGTGTAGTTTTTATTGCCATCCCTTCCAAAACCCAAACAGCGTCACCACACG
TCAAGTCAGTAGATGCTGTTGTGGTCCTTGGCATAAAGCTCAGCAGATATAACAAACGTACTCAATTTTCCATATGTGTT
GCTGGCCTTTTTGTATTTTACCTAATTTATGGATATTTACAGGAAATATTTTAGTGGAGAGCTTTAGGTCCTATGGCTGG
TACCTTACATTAGTGCAGTTTGGGTTTTACTCCATATTTGGCCTAATAGAACGTCGGCTTATTCAGGACAAAAGGAGAAT
ACTAGGAACAACCTACATGATGATGGCTTTTCTGAGTGGGGTTATGGGGTTATGAAACACTTCCTTGGGCTACCTGAATT
ATCCTACCCAAGTCATCTTCAAGTGCTGCAAATTAATTTCGGTTATGCTGAGAGTTGTTATTCAAGGAAAGCAATATAAC
ACTGCAGATGAGTCTGCTGCAGTGTCTATGAGCCTTGTCCGGATAAGGTTTACCCCGGCTGACCGCACAGTTGCACCGAA
TTTCGACCTGACGGGTGATCCTGTTTCCTCGGTACCATGTGCAGATGGCATTATTGGGAACATCTAAGAGAAAGCTATGA
GACTACATAATGCTGCTAATTTGGAAGTGGGTCTGTATTCGCATTCAGTAGGTTTTGTATATGCTTTATTGGGATTGACA
TGAACTAGCGGATTACACTCTGCAGTCACATTTTGTTCAAAGAATCCAATTCAGACCTATGGTTATGCCTCCCTTTTTCC
CCCTCGCGGGGTATTTTGGAATCTCCTTGTTCTGGCTTTGCTTAAAATTTTTGGTGCACTTGTTGCTATAATAGTGATAA
CAGAAAGAAAAGCGACGGCCATTGTACTTTCATTTGTATTTTTTGCTAGACCGTTAATATCGCAGGCTGTATGGCCTGGT
TAGTTGTCCTGGGTGTATTTGCAATGTTTACAGCAAAAATACGGACAAAATAAGACTACCATCACTACAAGGTCTGATAA
ATCAGTGGGTGAGAGAG

Alignment

ORF - retro_lafr_641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.68 %
• Parental protein coverage: 97.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MDLKFNNSRK-YISITVPSKTQAMSPHIKSIDDIVVLGINLSRFNKLTQFFICVAGVFVFYLIYGYLQEL
          MDLKF..SRK....I..PSKTQ..SPH.KS.D..VVLGI.LSR.NK.TQF.ICVAG.FVFYLIYGYLQE.
Retrocopy MDLKFSSSRK>VVFIAIPSKTQTASPHVKSVDAVVVLGIKLSRYNKRTQFSICVAGLFVFYLIYGYLQE-

Parental  IF-SVEGFKSYGWYLTLVQFGFYSTFGLIELQLIQDKRRRIPGKTYMTIAFLTVGTMGLSNTSLGYLNYP
          IF..VE.F.SYGWYLTLVQFGFYS.FGLIE..LIQDKRR.I.G.TYM..AFL..G.MGL.NTSLGYLNYP
Retrocopy IF<LVESFRSYGWYLTLVQFGFYSIFGLIERRLIQDKRR-ILGTTYMMMAFLS-GVMGL*NTSLGYLNYP

Parental  TQVIFKCCKLIPVMLGGVFIQGKRYNVADVSAAVCMSLGLIWFTLADSTIAPNFNLTGVILISLALCADA
          TQVIFKCCKLI.VML..V.IQGK.YN.AD.SAAV.MSL..I.FT.AD.T.APNF.LTG....S...CAD.
Retrocopy TQVIFKCCKLISVMLR-VVIQGKQYNTADESAAVSMSLVRIRFTPADRTVAPNFDLTGDPVSSVP-CADG

Parental  VIGNVQEKAMKLHNASNSEMVLYSYSIGFVYILLGLTCTSGLRPAVTFCSKNPVRTYGYAFL-FSLTGYF
          .IGN..EKAM.LHNA.N.E..LYS.S.GFVY.LLGLT.TSGL..AVTFCSKNP..TYGYA.L.F.L.GYF
Retrocopy IIGNI*EKAMRLHNAANLEVGLYSHSVGFVYALLGLT*TSGLHSAVTFCSKNPIQTYGYASL>FPLAGYF

Parental  GIS-FVLALIKIFGALLAVTVTTGRKAMTIVLSFMFFTKPFTFQYVWSG-LLVVLGIF-LNVYSKNMDKI
          GIS..VLAL.KIFGAL.A..V.T.RKA..IVLSF.FF..P...Q.VW.G.L.V.LG.F..NVYSKN.DKI
Retrocopy GIS<LVLALLKIFGALVAIIVITERKATAIVLSFVFFARPLISQAVWPG<LVV-LGVF<CNVYSKNTDKI

Parental  RLPSLQGLINKSVDE
          RLPSLQGLIN..V.E
Retrocopy RLPSLQGLINQWVRE

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_641 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002579	1 retrocopy	retro_lafr_641 ,
Procavia capensis	ENSPCAG00000006201	1 retrocopy	retro_pcap_65,