RetrogeneDB ID: retro_lafr_362

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_13:49903924..49904785(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IK
• Ensembl ID: ENSLAFG00000008152
• Aliases: None
• Description: None

Sequence

>retro_lafr_362
CCCACCTCTGCATGGCCCTTGAAGTCACATTACCCTTAGATACCTCTGGAGTACACTGAGGCTGAAGACCCAGCTGCATG
AAGGAGAAAAAGGGAGAGTTATTATGCCAACCTAGGACAATGAAAAAATTGAGAGAGAGTAGGAGCTAGCATAGATATAC
TAGGACCATGCCAAGGAATGTATAGGTGATGGGAACAAAGATTACAAGGGAATTGAGTTGATTAAGTACCACAGCTAACT
ACAGGGCTGTGGGCCCCACAGCTGAAGCAGACAGATCTTCACTCAGAGGAGAGAAAACAGTTGATCCAGGAGTCCAGATT
CTTAGATGGTGACATGGAACATACCCATTCAGTGAAAGGCTTAGATTTTTGCTCTACTTGAAAAGATTGGAGCTGATAAT
CCTGGCAAAGAGAAAGAGGAGGAGGAATTGATGGAAAAATTTCAGAAAGGAACCAAGAAAGATGAGGATCCTGAGAATAA
GACTGAATTTAAAATATGTCTGGCCTGCAATGTTTTCCCATACTCTTCTGAAGCAAAGCATACAACAATATCAAAGAGCT
GTTCCTGCCTGGCCACATGGCCTATGTGGTGGAGTTGGATGACAAGTATGCTGACATGGACATGCCCCTCACTCTAATCT
GCAGCAAGGCTGATTGTCCCAACATAGAAGTCCATACCACACTGACCACAAATGGCATTGTCATCAGTAAGCTCACCCAG
ATACTTTGCTACCTTAGTAAGAGGGCCTGCAATGAGAAGCTCAAGAAGAAGGACCAAGGAAAGCTGGAAGGGAAGAAACC
TCTTGAGGCCAATATGAAAATTTTTGAAGATGCTGAAGATTACACAGCCTCTATAGCCAGA

Alignment

ORF - retro_lafr_362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.01 %
• Parental protein coverage: 51.35 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PTSAPPSKSRHHEMPREYNEDEDPAARRRKKKSYYAKLRQ-QEIERERELAEKYRDRAKERRDGVNKDYE
          PTSA.P.KS.....P.EY.E.EDPAA.RRK..SYYA.L.Q...IERE.ELA..Y.D.AKE.....NKDY.
Retrocopy PTSAWPLKSHYP*IPLEYTEAEDPAA*RRKRESYYANLGQ>EKIERE*ELA*IY*DHAKECIGDGNKDYK

Parental  ETELI-STTANYRAVGPTAEADKSA-AEKRRQLIQESKFLGGDMEHTHLVKGLDF-ALLQKVRAEIASKE
          ..ELI.STTANYRAVGPTAEAD.S...E.R.QLIQES.FL.GDMEHTH.VKGLDF.ALL.K..A....KE
Retrocopy GIELI>STTANYRAVGPTAEADRSS>SEERKQLIQESRFLDGDMEHTHSVKGLDF>ALLEKIGADNPGKE

Parental  KEEEELMEKPQKETKKDEDPENKIEFKTRLGRNVYR-MLFKSKAYER-NELFLPGRMAYVVDLDDEYADT
          KEEEELMEK.QK.TKKDEDPENK.EFK..L..NV....LF.SKAY....ELFLPG.MAYVV.LDD.YAD.
Retrocopy KEEEELMEKFQKGTKKDEDPENKTEFKICLACNVFP<ILF*SKAYNNIKELFLPGHMAYVVELDDKYADM

Parental  DIPTTLIRSKADCPTMEAQTTLTTNDIVISKLTQILSYLRQGTRNKKLKKKDKGKLEEKKPPEADMNIFE
          D.P.TLI.SKADCP..E..TTLTTN.IVISKLTQIL.YL.....N.KLKKKD.GKLE.KKP.EA.M.IFE
Retrocopy DMPLTLICSKADCPNIEVHTTLTTNGIVISKLTQILCYLSKRACNEKLKKKDQGKLEGKKPLEANMKIFE

Parental  DVGDYVPSTTK
          D..DY..S...
Retrocopy DAEDYTASIAR

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_362 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009727	3 retrocopies	retro_dnov_618, retro_dnov_714, retro_dnov_960,
Dipodomys ordii	ENSDORG00000006584	4 retrocopies	retro_dord_128, retro_dord_130, retro_dord_134, retro_dord_139,
Homo sapiens	ENSG00000113141	1 retrocopy	retro_hsap_2262,
Gorilla gorilla	ENSGGOG00000013374	1 retrocopy	retro_ggor_1685,
Loxodonta africana	ENSLAFG00000008152	1 retrocopy	retro_lafr_362 ,
Otolemur garnettii	ENSOGAG00000014281	1 retrocopy	retro_ogar_1402,
Pongo abelii	ENSPPYG00000015861	1 retrocopy	retro_pabe_1954,
Sorex araneus	ENSSARG00000007388	3 retrocopies	retro_sara_416, retro_sara_419, retro_sara_558,