RetrogeneDB ID: retro_lafr_472

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_18:39573958..39574528(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL19
• Ensembl ID: ENSLAFG00000000146
• Aliases: None
• Description: None

Sequence

>retro_lafr_472
GTAGAAAGGAGGAAGGTACTACACATTCCAGAGTTCTATGTCAGAAGCATACTTCGTGTTACTACAGCAGACTCTTATGC
CGGTGGAAAAATCAGCCAGTTTCTGGGGATTTGCATCCAGAGATCAGAAAAAGGACTTGGAGCTACCTTTATCCTTAGGA
ATACTATTGAAGGACAAGGTGTTGAGATTTGCTTTCAACTTTATAATCCCCGAATTCAGGAGATCCAAGTGGTCAAATCA
GAGAAACGGCTGGATGACAGCTTGCTGTACTTAAGAGATGCCCTTCCTGAATACAGCACTTTTGATAGGAACATGGAGCC
AGTAGCACATGAATCTGACCAAGAAGTTCCTGTGAATCAGCTGAAAGTAAAAATGAAGCCTAAGCCCTGGTCCAAACGCT
GGTAACGTCCAAAATTTAATGTGAAAGGAATCCAGTTTGATCTTTATTTAACTGAAGAGCAAATAAAAGAAGCTCAGAAG
TGGGGTCAGCCTTGGCTTGAGTTTGATATGATGAGGGAATATGACACTTCACAAACTGAAGCTGCAATATGGGATGAAAT
CGAAGCATCG

Alignment

ORF - retro_lafr_472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.23 %
• Parental protein coverage: 64.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LERRKVLHIPEFYVELVGSILRVTTADPYANGKMSEFLGICIQRSGKGLGATFILRNTIEGQGVEICFQL
          .ERRKVLHIPEFYV....SILRVTTAD.YA.GK.S.FLGICIQRS.KGLGATFILRNTIEGQGVEICFQL
Retrocopy VERRKVLHIPEFYVR---SILRVTTADSYAGGKISQFLGICIQRSEKGLGATFILRNTIEGQGVEICFQL

Parental  YNPRIQEIQVVKLEKRLDDSLLYLRDALPEYSTFDRNMKPVAHESDQEVPVNQLKVKMKPKPWSKRWERP
          YNPRIQEIQVVK.EKRLDDSLLYLRDALPEYSTFDRNM.PVAHESDQEVPVNQLKVKMKPKPWSKRW.RP
Retrocopy YNPRIQEIQVVKSEKRLDDSLLYLRDALPEYSTFDRNMEPVAHESDQEVPVNQLKVKMKPKPWSKRW*RP

Parental  KFNVKGIQFDLYLTEEQMKEAQKWGQPWLEFDMMREYDTSQTEAAIWGEIEAS
          KFNVKGIQFDLYLTEEQ.KEAQKWGQPWLEFDMMREYDTSQTEAAIW.EIEAS
Retrocopy KFNVKGIQFDLYLTEEQIKEAQKWGQPWLEFDMMREYDTSQTEAAIWDEIEAS

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_472 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002266	1 retrocopy	retro_eeur_485,
Homo sapiens	ENSG00000115364	1 retrocopy	retro_hsap_2957,
Gorilla gorilla	ENSGGOG00000027896	1 retrocopy	retro_ggor_2048,
Loxodonta africana	ENSLAFG00000000146	1 retrocopy	retro_lafr_472 ,
Myotis lucifugus	ENSMLUG00000012774	1 retrocopy	retro_mluc_1308,
Pongo abelii	ENSPPYG00000012255	1 retrocopy	retro_pabe_2453,
Pan troglodytes	ENSPTRG00000012108	1 retrocopy	retro_ptro_2002,
Ictidomys tridecemlineatus	ENSSTOG00000002873	1 retrocopy	retro_itri_549,
Tupaia belangeri	ENSTBEG00000016470	1 retrocopy	retro_tbel_326,