RetrogeneDB ID: retro_lafr_432

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_16:2850671..2850995(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000032069
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDHD
• Ensembl ID: ENSLAFG00000002763
• Aliases: None
• Description: None

Sequence

>retro_lafr_432
GCGGTGCTCTGGAGGCTGAGCATCCCCTGTGGTTCCCACGGAGCCAGAGCTCTCTTCCTCTGAACCCCAGTGGTCAGACA
TGCCCATGTCTCAGCATTTCTCCAGGATAGGCCTACCTCAGGAGCACAGCACATCTACCTGTCCATCAGCCACCATTCTG
GTTCCAAGGTTGCATTTCTCCACTGGACTGGCGAGAGGGTTGTCAGTGTTTTGCTCCTGGGCCTGCACCCACCTGCTTAT
TTGAATCCTTGCTCAGTGATGGACTACTCCCTGGCTGCAGCCCTTACTCCCCATAGTCACAAGGGTATTGGACAAGTTGT
TACT

Alignment

ORF - retro_lafr_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVLWRLSVFCGPQGARAPFFRTPVVRPAQVSAFLQDRSTPGVQHIHLSPRHHSASKAASLHWTGERVVSV
          AVLWRLS..CG..GARA.F..TPVVR.A.VSAFLQDR.T.G.QHI.LS..HHS.SK.A.LHWTGERVVSV
Retrocopy AVLWRLSIPCGSHGARALFL*TPVVRHAHVSAFLQDRPTSGAQHIYLSISHHSGSKVAFLHWTGERVVSV

Parental  LLLGLLPAAYLNPCPAMDYSLAAALTLHSHWGIGQVVT
          LLLGL.P.AYLNPC..MDYSLAAALT.HSH.GIGQVVT
Retrocopy LLLGLHPPAYLNPCSVMDYSLAAALTPHSHKGIGQVVT

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_432 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 15 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004066	3 retrocopies	retro_amel_1556, retro_amel_1588, retro_amel_998,
Callithrix jacchus	ENSCJAG00000010975	4 retrocopies	retro_cjac_1385, retro_cjac_1390, retro_cjac_1557, retro_cjac_3829,
Erinaceus europaeus	ENSEEUG00000013091	1 retrocopy	retro_eeur_336,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252,
Felis catus	ENSFCAG00000022580	3 retrocopies	retro_fcat_1371, retro_fcat_175, retro_fcat_492,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355, retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432 ,
Myotis lucifugus	ENSMLUG00000012228	3 retrocopies	retro_mluc_2418, retro_mluc_457, retro_mluc_756,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224,
Otolemur garnettii	ENSOGAG00000008568	5 retrocopies	retro_ogar_1651, retro_ogar_1795, retro_ogar_2087, retro_ogar_3122, retro_ogar_3147,
Pongo abelii	ENSPPYG00000003876	5 retrocopies	retro_pabe_1549, retro_pabe_1924, retro_pabe_2233, retro_pabe_2999, retro_pabe_3096,
Rattus norvegicus	ENSRNOG00000022980	3 retrocopies	retro_rnor_1529, retro_rnor_1686, retro_rnor_744,
Sus scrofa	ENSSSCG00000015034	3 retrocopies	retro_sscr_1060, retro_sscr_626, retro_sscr_627,
Tursiops truncatus	ENSTTRG00000010520	5 retrocopies	retro_ttru_1554, retro_ttru_238, retro_ttru_616, retro_ttru_633, retro_ttru_885,