RetrogeneDB ID: retro_lafr_706

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_31:14218449..14219152(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12ORF29
• Ensembl ID: ENSLAFG00000013286
• Aliases: None
• Description: None

Sequence

>retro_lafr_706
TTTAAAAATTCTATATTCGAAAGAAAGTTCAAAATAGTATTTTTTTGGAATACTGAGGAGGACTTGCAACCTGTCGCAGG
GGGCTGGATACCAGTGAAGGAAACAGGACATTTACATGGGAAACCAGTCCCTCACGCAACTGGACACATTCCTGGTGGGG
TACCAGTAGAAAAAAACAATAAACAATATTGTTGGCATTCCTCTGTAGTTAAATCTGAATTTGAAATCACTCTGGTAATG
AAGCATCATCCTGACGATCCAGGACTTTTGGAAATTGGTGCAGTGCCACTATCAGATATGTTAGAACAAACACTGGAGCT
TATAGGAACAAATGTTAATGGAAACCCATATGGGTTAGGAAGTAAGAAGCATGCATTACATCTTCTTAAACCACAGGGAG
CATTTCAAGTAAGAAATCTGCCTACAATGAGGCACAGTGATCTGTTGTCCTGGTTGAAGGGTGCAGAGACGGTAAAATTG
AAGGAATAGTACGGCATTGCAATGATGGCTGTTTAATCAAGGTCCATCACTGTCATCTTGGTTTACATTGGCCAATTCCA
GATATTTACATGAATTCAAAACCAGTTATTATCAACAGGGACCTGAACAAATATGATTATGCCTTTGATTCTAAATGTTT
ATTTACTTATTTTTCAAAAATAGACAATCAGAAATTTGCAGGCTCAAAGAGATAAGGTTCGAT

Alignment

ORF - retro_lafr_706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.95 %
• Parental protein coverage: 72.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FKKFLYSKENSKEFFWNVEEDFKPVPECWIPAKEIEQLDGKPVPDENGHIPGWVPVEKNNKQYCWHSSVV
          FK...........FFWN.EED..PV...WIP.KE...L.GKPVP...GHIPG.VPVEKNNKQYCWHSSVV
Retrocopy FKNSIFERKFKIVFFWNTEEDLQPVAGGWIPVKETGHLHGKPVPHATGHIPGGVPVEKNNKQYCWHSSVV

Parental  NYEFDIALVLKHHPDDPGLLEISAVPLSDLLEQTLELIGTNINGNPYGLGSKKHPLHLLIPHGAFHIRNL
          ..EF.I.LV.KHHPDDPGLLEI.AVPLSD.LEQTLELIGTN.NGNPYGLGSKKH.LHLL.P.GAF..RNL
Retrocopy KSEFEITLVMKHHPDDPGLLEIGAVPLSDMLEQTLELIGTNVNGNPYGLGSKKHALHLLKPQGAFQVRNL

Parental  PTLKHNDLLSWF-ESCREGKIEGIVWHCNDGCLIKVHRHHLGLHWPIPDTFMNSKPVIINMDLNKYDYAF
          PT..H.DLLSW..E.CR.GKIEGIV.HCNDGCLIKVH..HLGLHWPIPD..MNSKPVIIN.DLNKYDYAF
Retrocopy PTMRHSDLLSWL<EGCRDGKIEGIVRHCNDGCLIKVHHCHLGLHWPIPDIYMNSKPVIINRDLNKYDYAF

Parental  DSKCLFSYFSKIDNQKFS-RLKDIMFD
          DSKCLF.YFSKIDNQKF..RLK.I.FD
Retrocopy DSKCLFTYFSKIDNQKFA<RLKEIRFD

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_706 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011011	1 retrocopy	retro_chof_1262,
Homo sapiens	ENSG00000133641	1 retrocopy	retro_hsap_3984,
Gorilla gorilla	ENSGGOG00000005986	1 retrocopy	retro_ggor_2674,
Loxodonta africana	ENSLAFG00000013286	1 retrocopy	retro_lafr_706 ,
Macaca mulatta	ENSMMUG00000015860	1 retrocopy	retro_mmul_715,
Nomascus leucogenys	ENSNLEG00000005396	1 retrocopy	retro_nleu_1905,
Pan troglodytes	ENSPTRG00000005277	1 retrocopy	retro_ptro_2704,
Rattus norvegicus	ENSRNOG00000006973	1 retrocopy	retro_rnor_1625,
Tupaia belangeri	ENSTBEG00000005256	1 retrocopy	retro_tbel_94,
Tarsius syrichta	ENSTSYG00000014665	1 retrocopy	retro_tsyr_1572,