RetrogeneDB ID: retro_lafr_411

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:46940615..46940994(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORMDL1
• Ensembl ID: ENSLAFG00000007769
• Aliases: None
• Description: None

Sequence

>retro_lafr_411
GCCGTGGGAGTTGGCATCGCTTCATGTTGTCTTACTCAGCATTCCCTTCTTCAGTGTTCCTGTTGCTTGGACCTTAACAA
ATACGTAGAACTTGGGGATGTATGTATTTTTGCATGCAGTGAAAGGAACGCCTTTTGGAACTCCTGACCAGGGTAAAGCA
AGACGCCTAACTCATTGGAAACAACTCACCTATAGAGTAGAGTTTATATCTTCATGGAAGTTTTTCATAATTTGTCCAAT
GATTCTGTATTTCCTGGAAAGTTTCTATTTGAAGTATGATCCAACTCATTTTACCCTAAAAACAGCTTCTCTCCTAAGTG
TGCTAATTCCCAAAATGCCACAACTACATGGTGTTCAGACCTTTGGAATTAATAAGTAT

Alignment

ORF - retro_lafr_411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 83.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALGVGL-LHIVLLSIPFFSVPVAWTLTNIIHNLGMYVFLHAVKGTPFETPDQGKARLLTHWEQLDYGVQF
          A.GVG..LH.VLLSIPFFSVPVAWTLTN...NLGMYVFLHAVKGTPF.TPDQGKAR.LTHW.QL.Y.V.F
Retrocopy AVGVGI>LHVVLLSIPFFSVPVAWTLTNT*-NLGMYVFLHAVKGTPFGTPDQGKARRLTHWKQLTYRVEF

Parental  TSSRKFFTISPIILYFLASFYTKYDPTHFILNTASLLSVLIPKMPQLHGVRIFGINKY
          .SS.KFF.I.P.ILYFL.SFY.KYDPTHF.L.TASLLSVLIPKMPQLHGV..FGINKY
Retrocopy ISSWKFFIICPMILYFLESFYLKYDPTHFTLKTASLLSVLIPKMPQLHGVQTFGINKY

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_411 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005579	1 retrocopy	retro_cjac_2962,
Homo sapiens	ENSG00000128699	1 retrocopy	retro_hsap_645,
Gorilla gorilla	ENSGGOG00000015259	1 retrocopy	retro_ggor_565,
Loxodonta africana	ENSLAFG00000007769	1 retrocopy	retro_lafr_411 ,
Myotis lucifugus	ENSMLUG00000014339	1 retrocopy	retro_mluc_2318,
Macaca mulatta	ENSMMUG00000014316	1 retrocopy	retro_mmul_2432,
Nomascus leucogenys	ENSNLEG00000006625	1 retrocopy	retro_nleu_730,
Pongo abelii	ENSPPYG00000013017	2 retrocopies	retro_pabe_570, retro_pabe_571,
Pan troglodytes	ENSPTRG00000012736	1 retrocopy	retro_ptro_469,
Sus scrofa	ENSSSCG00000016044	1 retrocopy	retro_sscr_247,
Tupaia belangeri	ENSTBEG00000012942	1 retrocopy	retro_tbel_10,
Tursiops truncatus	ENSTTRG00000005240	2 retrocopies	retro_ttru_1846, retro_ttru_770,