RetrogeneDB ID: retro_lafr_1067

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_64:1710431..1710769(-)
• Located in intron of: ENSLAFG00000011779

Retrocopy information

• Ensembl ID: ENSLAFG00000025824
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TDGF1
• Ensembl ID: ENSLAFG00000009140
• Aliases: None
• Description: None

Sequence

>retro_lafr_1067
TTCACGGGAATCCAGGACAGCAAAGAGCTGAACAAGACCTGCTGTCTGAACAGGGGAACCTGGACCCTGGGATTCTTTTG
CGCTTGCATTCCTTACTTCTACGGATGAACTGTGAGCATGATTTTTGCAAAGTGAATTGTAGGTGTGCGCCCCATGACAC
CTGCCTGCCCAAGAAGTGTTCCATGTGTAAATGCTGGCATGACTGGCTTCAGTGCTTTGCTCAGACATTTTTACCTGGTT
GTGATAATCATGTGATAGATGAGCACCTCATGGCTTCCAGGACTCCAGAATTAATGTCATCTGCATGCACCACTCTTATG
CTAGTTGGCATCTGCCTT

Alignment

ORF - retro_lafr_1067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.56 %
• Parental protein coverage: 70.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FMGIQDSKELNKTCCLNGGTCMLGSFCACPPYFYG-RNCEHDVRKENCGSVPHDTWLPRKCSMCKCWHGW
          F.GIQDSKELNKTCCLN.GT..LG.FCAC.PYFYG..NCEHD..K.NC...PHDT.LP.KCSMCKCWH.W
Retrocopy FTGIQDSKELNKTCCLNRGTWTLGFFCACIPYFYG<MNCEHDFCKVNCRCAPHDTCLPKKCSMCKCWHDW

Parental  LRCFPQTFLPGCDGRVMDEHLEASRTPELLPSVCTTLMLASLCL
          L.CF.QTFLPGCD..V.DEHL.ASRTPEL..S.CTTLML...CL
Retrocopy LQCFAQTFLPGCDNHVIDEHLMASRTPELMSSACTTLMLVGICL

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_1067 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 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002174	3 retrocopies	retro_cjac_1594, retro_cjac_4151, retro_cjac_938,
Felis catus	ENSFCAG00000014508	1 retrocopy	retro_fcat_714,
Homo sapiens	ENSG00000241186	7 retrocopies	retro_hsap_1999, retro_hsap_2393, retro_hsap_2709, retro_hsap_3415, retro_hsap_3956, retro_hsap_4737, retro_hsap_4804,
Gorilla gorilla	ENSGGOG00000003453	5 retrocopies	retro_ggor_1447, retro_ggor_1815, retro_ggor_2307, retro_ggor_2943, retro_ggor_2990,
Loxodonta africana	ENSLAFG00000009140	4 retrocopies	retro_lafr_1037, retro_lafr_1067 , retro_lafr_757, retro_lafr_871,
Microcebus murinus	ENSMICG00000016492	1 retrocopy	retro_mmur_635,
Macaca mulatta	ENSMMUG00000003088	6 retrocopies	retro_mmul_1744, retro_mmul_2290, retro_mmul_2560, retro_mmul_742, retro_mmul_770, retro_mmul_967,
Mustela putorius furo	ENSMPUG00000015167	1 retrocopy	retro_mputfur_961,
Mus musculus	ENSMUSG00000032494	3 retrocopies	retro_mmus_1429, retro_mmus_1544, retro_mmus_1908,
Nomascus leucogenys	ENSNLEG00000006143	6 retrocopies	retro_nleu_1649, retro_nleu_2124, retro_nleu_2179, retro_nleu_2317, retro_nleu_2519, retro_nleu_535,
Otolemur garnettii	ENSOGAG00000017039	1 retrocopy	retro_ogar_2611,
Pan troglodytes	ENSPTRG00000014854	7 retrocopies	retro_ptro_1333, retro_ptro_1749, retro_ptro_1831, retro_ptro_2319, retro_ptro_2685, retro_ptro_3153, retro_ptro_3194,
Tarsius syrichta	ENSTSYG00000013609	2 retrocopies	retro_tsyr_295, retro_tsyr_574,
Tursiops truncatus	ENSTTRG00000017299	1 retrocopy	retro_ttru_441,