RetrogeneDB ID: retro_lafr_242

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:32964618..32965008(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRELID1
• Ensembl ID: ENSLAFG00000005459
• Aliases: None
• Description: None

Sequence

>retro_lafr_242
AAGTATTTCCTGGGTCAGAGCATGCTCCAGAGTTCCTGGGACCAAGAGTTCACTGACTTCTGGCGGCGGTACCAGAACCC
CTACAGCAAACATGTCACGCTGGAAGATATAGTACACCTGAAGGTGACCTCTGACCAGAAGCTCCTGTCCTGACAACTCC
TGACCAAGACTAACAGGATGCCCTGCTGGGCCTGGTAACTGTTTCCTTCCAATGTTGCTCACTAGGTGTACATCCTGGAG
GACTCTATTGTGGACCCACAGAATCAGAACATGAACACCTGTACCTGGAACATCAACCACAGCAGGCTGGTGGTGGTGGA
GGGATGCTGTATTTACTACGTGAACTCTAATAACAGCTACTTGACTGAAATCTGCTGGGAAGCATGGGTT

Alignment

ORF - retro_lafr_242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.62 %
• Parental protein coverage: 59.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYFLGQSVLRSSWDQVFAAFWQRYPNPYSKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERLFPA
          KYFLGQS.L.SSWDQ.F..FW.RY.NPYSKHV..EDIVH..VT.DQKLLS..LLTKTNRMP.WA..LFP.
Retrocopy KYFLGQSMLQSSWDQEFTDFWRRYQNPYSKHVTLEDIVHLKVTSDQKLLS*QLLTKTNRMPCWAW*LFPS

Parental  NVAHSVYILEDSIVDPQNQTMTTFTWNINHARLMVVEERCVYCVNSDNSGWTEIRREAWV
          NVAH.VYILEDSIVDPQNQ.M.T.TWNINH.RL.VVE..C.Y.VNS.NS..TEI..EAWV
Retrocopy NVAH*VYILEDSIVDPQNQNMNTCTWNINHSRLVVVEGCCIYYVNSNNSYLTEICWEAWV

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_242 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.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Loxodonta africana	ENSLAFG00000005459	1 retrocopy	retro_lafr_242 ,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,