RetrogeneDB ID: retro_lafr_1115

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_7:74152936..74153342(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000006176
• Aliases: None
• Description: None

Sequence

>retro_lafr_1115
GACTCTCTCAAGGCTCTAGCTCGTGATGTTCCTATTGTGAGAGAAGACTTTGATGGAAATCTGAATTATTCAGAACAGAA
AGTTGCGACTATTGGACAGTTCAAAATTGGTTTGATCCATGGACATCAAGTTATTTGCTGGGGAGATATGGCCAGCTTAG
CCCTGTTGCAGAGGAGTTTGATGTGAATGTTCTTATTTCAGAATACACACACAAACTTGAAGCATTTGGGTATGAAAATA
AATTTACATTAACCCAGGCTCTGCCACTGGAGCATCTAATGCCTTGGAAACAAACATTATTCCTTCATTCATGTTGATGG
ACATCCAGGCTTCTACAGTTGTCACTTACGTGTACCAGCTAATTGGAGGTGTTGTGAAAGTAGAACAAACTGAATACAAA
AAATCT

Alignment

ORF - retro_lafr_1115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.16 %
• Parental protein coverage: 74.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQR-QFDVDILISGH
          D.LK.LA.DV.IVR.DFD.NLNY.EQKV.T.GQFKIGLIHGHQVI.WGDMASLALLQR..FDV..LIS..
Retrocopy DSLKALARDVPIVREDFDGNLNYSEQKVATIGQFKIGLIHGHQVICWGDMASLALLQR<EFDVNVLISEY

Parental  THKFEAFEHENKF-YINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS
          THK.EAF..ENKF.YINPGSATGA.NALETNIIPSF.LMDIQASTVVTYVYQLIG..VKVE..EYKKS
Retrocopy THKLEAFGYENKF<YINPGSATGASNALETNIIPSFMLMDIQASTVVTYVYQLIGGVVKVEQTEYKKS

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_1115 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001891	1 retrocopy	retro_acar_30,
Felis catus	ENSFCAG00000004135	2 retrocopies	retro_fcat_165, retro_fcat_848,
Loxodonta africana	ENSLAFG00000006176	1 retrocopy	retro_lafr_1115 ,
Monodelphis domestica	ENSMODG00000011577	1 retrocopy	retro_mdom_450,
Oryctolagus cuniculus	ENSOCUG00000011924	1 retrocopy	retro_ocun_1611,
Procavia capensis	ENSPCAG00000012049	1 retrocopy	retro_pcap_158,
Tupaia belangeri	ENSTBEG00000012756	4 retrocopies	retro_tbel_1121, retro_tbel_2187, retro_tbel_330, retro_tbel_4424,
Tursiops truncatus	ENSTTRG00000015090	2 retrocopies	retro_ttru_1404, retro_ttru_1492,