RetrogeneDB ID: retro_lafr_1214

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:34512184..34512670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSLAFG00000013251
• Aliases: None
• Description: None

Sequence

>retro_lafr_1214
ATGGTGCCGTCCAGGAGTCTCATGGTTTCCCTGGCAGTGCTGGTGGTATTACTATGGTGGACTCCCTGGACCCACGGGTG
GTGGAGTGACGTGCGCATCATCACAGACAAAAACTGGAAAGAGTTGCTGGGAAGGAAAGTGAATGATAGAATTTTATGTT
CCATGCCTGCTTGTCAAAATCTTCAACCAGAATGGGAAAGTCTTGCTGAATGGGGAGAAGATCTTGAGGTTAATGTTGCA
AAAGTAGATGTCATAAAGCAGCCAGGACCGAGGGGATGATTTATAATAACTTCTCTTCCTACTATTTATCGTTGTAAACA
TGGTGAATTTAGGTGTTATCAGGGCCTGAGGGCTAAGAAGGGCTTCATAAACTTTGTAAGTGAAAAAGAATGGAAGAATA
TTGGACCTGTTTCGTCATGGTTTGGTCTAGGTTCTATTCTGGTAAGTAGTATGTCAGCACTCTTTCAGTTATCTATGTGG
ATCAGG

Alignment

ORF - retro_lafr_1214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.18 %
• Parental protein coverage: 58.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALSRSLAVSLAILVVLLWWAPTTHARRSDVRIITDGNWKELL-EGEWMIEFYAPWC-PACQNLQPEWES
          M..SRSL.VSLA.LVVLLWW.P.TH...SDVRIITD.NWKELL.EG..MIEFY.P.C.PACQNLQPEWES
Retrocopy MVPSRSLMVSLAVLVVLLWWTPWTHGWWSDVRIITDKNWKELL>EGK*MIEFYVP-C<PACQNLQPEWES

Parental  FAEWGEDLEVNVGKVDVTEQPGLSGRFIITALPTIYHCKDGEFRRYQGPRTKKDFINFISEKEWKSIEPV
          .AEWGEDLEVNV.KVDV..QPG..G.FIIT.LPTIY.CK.GEFR.YQG.R.KK.FINF.SEKEWK.I.PV
Retrocopy LAEWGEDLEVNVAKVDVIKQPGPRG*FIITSLPTIYRCKHGEFRCYQGLRAKKGFINFVSEKEWKNIGPV

Parental  SSWFGPGSVLMSSMSALFQLSMWIR
          SSWFG.GS.L.SSMSALFQLSMWIR
Retrocopy SSWFGLGSILVSSMSALFQLSMWIR

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_1214 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015041	1 retrocopy	retro_amel_719,
Canis familiaris	ENSCAFG00000014626	1 retrocopy	retro_cfam_796,
Choloepus hoffmanni	ENSCHOG00000011305	1 retrocopy	retro_chof_1249,
Callithrix jacchus	ENSCJAG00000006893	1 retrocopy	retro_cjac_1453,
Dasypus novemcinctus	ENSDNOG00000016496	1 retrocopy	retro_dnov_78,
Felis catus	ENSFCAG00000002780	1 retrocopy	retro_fcat_333,
Homo sapiens	ENSG00000139921	2 retrocopies	retro_hsap_3840, retro_hsap_3970,
Gorilla gorilla	ENSGGOG00000009768	1 retrocopy	retro_ggor_2587,
Loxodonta africana	ENSLAFG00000013251	1 retrocopy	retro_lafr_1214 ,
Macaca mulatta	ENSMMUG00000001901	1 retrocopy	retro_mmul_1618,
Nomascus leucogenys	ENSNLEG00000012362	2 retrocopies	retro_nleu_1976, retro_nleu_2524,
Oryctolagus cuniculus	ENSOCUG00000003980	1 retrocopy	retro_ocun_571,
Pongo abelii	ENSPPYG00000005810	2 retrocopies	retro_pabe_3058, retro_pabe_3264,
Pan troglodytes	ENSPTRG00000006339	2 retrocopies	retro_ptro_2522, retro_ptro_2695,