RetrogeneDB ID: retro_lafr_1116

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_7:82349300..82349885(-)
• Located in intron of: ENSLAFG00000018061

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRIX1
• Ensembl ID: ENSLAFG00000007249
• Aliases: None
• Description: None

Sequence

>retro_lafr_1116
CTGAAAGGTTGTCGAACTCGTTTGTCTTTTGACCCTGCTTTTGATAAATTACCACATTATGCTTTGTAAAAAGAACTCTT
AATTCAGATCTTTCGTACACCACGGTATCATCCCAAAAGCCAGCCATTTGTGGACCATGTGTTTACTTTCACCATTTTGG
ATAATAGGATACGGTTTTGAAGCTTTCTGATTATAGAGGAAGATGCTGATCTTGTAGAAAGAGGACCTTGTTTTGTCTTA
AATCTCATAAAGATTTTCCAGGGAGGTTTTGGAGGACCAACTTCATATGAAAATCCTCACTACCAGTCACCAAACATGCA
TAGCTGTATCATAAGATCCATCACAGCTGTGAAATACAAAGAGAAACAGCAAGTGAAAGATGTGCAGAAACTGAGAAAGA
AAGGACCAAAGACTATTCTACCATATGGTCTCACTGCACATGTTTTCGTTACACCAGCTGAGGAAAAACCGATAGAAATA
CAGTGGGTAAAACCAGAACCGAAAGTTGATTTGAAAGCAAGAAAGAAAAGGATACACAAACGGCAAAGAAAAATGAAACA
GAAGATGAACAGGAGGAGTGCAAAA

Alignment

ORF - retro_lafr_1116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.13 %
• Parental protein coverage: 55.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKGSRPLLSFDPAFDELPHYALLKELLIQIFCTPRYHPKSQPFVDHVFTFTILDNRIWFRNFQIIEEDAA
          LKG.R..LSFDPAFD.LPHYAL.KELLIQIF.TPRYHPKSQPFVDHVFTFTILDNRI.F..F.IIEEDA.
Retrocopy LKGCRTRLSFDPAFDKLPHYAL*KELLIQIFRTPRYHPKSQPFVDHVFTFTILDNRIRF*SFLIIEEDAD

Parental  LVEIGPRFVLNLIKIFQGSFGGPTLYENPHYQSPNMHRRIMRSITAVKYKEKQQVKEVQKLRKKEPKTIL
          LVE.GP.FVLNLIKIFQG.FGGPT.YENPHYQSPNMH..I.RSITAVKYKEKQQVK.VQKLRKK.PKTIL
Retrocopy LVERGPCFVLNLIKIFQGGFGGPTSYENPHYQSPNMHSCIIRSITAVKYKEKQQVKDVQKLRKKGPKTIL

Parental  PHDPTADVFVIPAEEKPIEIEWVKPEPKVDLKARKKRIYKRQRKMKQKMNSGSAK
          P...TA.VFV.PAEEKPIEI.WVKPEPKVDLKARKKRI.KRQRKMKQKMN..SAK
Retrocopy PYGLTAHVFVTPAEEKPIEIQWVKPEPKVDLKARKKRIHKRQRKMKQKMNRRSAK

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_1116 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 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001790	2 retrocopies	retro_chof_1664, retro_chof_1776,
Callithrix jacchus	ENSCJAG00000018506	1 retrocopy	retro_cjac_1389,
Homo sapiens	ENSG00000113460	1 retrocopy	retro_hsap_3954,
Gorilla gorilla	ENSGGOG00000004225	1 retrocopy	retro_ggor_2657,
Loxodonta africana	ENSLAFG00000007249	1 retrocopy	retro_lafr_1116 ,
Myotis lucifugus	ENSMLUG00000029255	3 retrocopies	retro_mluc_1402, retro_mluc_707, retro_mluc_963,
Macaca mulatta	ENSMMUG00000000442	1 retrocopy	retro_mmul_2289,
Monodelphis domestica	ENSMODG00000020386	1 retrocopy	retro_mdom_1032,
Nomascus leucogenys	ENSNLEG00000014452	1 retrocopy	retro_nleu_533,
Otolemur garnettii	ENSOGAG00000014827	2 retrocopies	retro_ogar_3116, retro_ogar_793,
Pongo abelii	ENSPPYG00000015390	2 retrocopies	retro_pabe_3258, retro_pabe_3379,
Pan troglodytes	ENSPTRG00000016784	1 retrocopy	retro_ptro_2684,
Rattus norvegicus	ENSRNOG00000018021	1 retrocopy	retro_rnor_1140,
Tupaia belangeri	ENSTBEG00000011652	9 retrocopies	retro_tbel_1963, retro_tbel_1964, retro_tbel_2981, retro_tbel_3002, retro_tbel_3082, retro_tbel_4194, retro_tbel_4229, retro_tbel_4418, retro_tbel_954,