RetrogeneDB ID: retro_lafr_379

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_14:52398701..52398970(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000032060
• Aliases: None
• Description: None

Sequence

>retro_lafr_379
AAGGAGAAGATCAACGCGCTCATTAAAGATCTGGTGTAAATGTGGAACCTTTCTGGGCTGGCTGGTTTGCAAATGCCCTG
GTCAACGTGAACATGAGAAGTCTCATCTGCAAAGGAGGGGCTGGTGGACCTCTGGCCACAAGGAGCACTGCACTAGTGGG
AGGACCTGTCCTCTCCAGCCCTGCTGTATCAGCTGAGGAGAAGAAAGTGGAAGCAAAGAATGAAGAATGTAAGGTATCTC
CTGATGACATGGACCTTGGTCTTTTTGAC

Alignment

ORF - retro_lafr_379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDKINALIK-AAGVNVEPFWPGLFAKALANVNVGSLICNVGAGGPAPAAGPAPAGGPAPSTAAAPAEEKK
          ..KINALIK...GVNVEPFW.G.FA.AL.NVN..SLIC..GAGGP......A..GGP..S..A..AEEKK
Retrocopy KEKINALIK<RSGVNVEPFWAGWFANALVNVNMRSLICKGGAGGPLATRSTALVGGPVLSSPAVSAEEKK

Parental  VEAKKEESEESDDDMGFGLFD
          VEAK.EE...S.DDM..GLFD
Retrocopy VEAKNEECKVSPDDMDLGLFD

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_379 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 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000012630	1 retrocopy	retro_lcha_7,
Loxodonta africana	ENSLAFG00000032060	3 retrocopies	retro_lafr_379 , retro_lafr_52, retro_lafr_71,
Macropus eugenii	ENSMEUG00000015277	6 retrocopies	retro_meug_1096, retro_meug_1283, retro_meug_1312, retro_meug_1401, retro_meug_1515, retro_meug_793,
Monodelphis domestica	ENSMODG00000009209	1 retrocopy	retro_mdom_1022,
Oryctolagus cuniculus	ENSOCUG00000015087	8 retrocopies	retro_ocun_1009, retro_ocun_1464, retro_ocun_1655, retro_ocun_1735, retro_ocun_48, retro_ocun_551, retro_ocun_647, retro_ocun_884,
Ochotona princeps	ENSOPRG00000001163	11 retrocopies	retro_opri_1010, retro_opri_130, retro_opri_214, retro_opri_245, retro_opri_38, retro_opri_530, retro_opri_645, retro_opri_768, retro_opri_784, retro_opri_96, retro_opri_972,
Sarcophilus harrisii	ENSSHAG00000014818	6 retrocopies	retro_shar_182, retro_shar_234, retro_shar_449, retro_shar_550, retro_shar_614, retro_shar_742,
Tarsius syrichta	ENSTSYG00000013927	1 retrocopy	retro_tsyr_82,