RetrogeneDB ID: retro_lafr_858

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_40:3628551..3628831(-)
• Located in intron of: ENSLAFG00000000838

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000025811
• Aliases: None
• Description: None

Sequence

>retro_lafr_858
ATGGCAGGCGGAAAACCCAAGGAAGGCATCAAGACTGAGAACAACAATCATATTAATTTGAAGGTGGAAGGCATGATGGT
TCTGTGGTACAGTTTAAGATTAAGAGGCATACACCAGTTAGTAAACTAATGAAAGTCTATTGTGAACAGGGTTTGTCAAA
GAGGCGGACCAAATTTGATTTCATGGGCAGCCAATCAATGACACAAACACAACTGCACAGTTGTAAATGGAGGATGAAAA
TACAACTGATGTGTTCCTGCGGCAGACAGGAGGTGTCTTC

Alignment

ORF - retro_lafr_858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADEKPKEGVKTENNDHINLKVAGQ-DGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRF-DGQPIN
          MA..KPKEG.KTENN.HINLKV.G..DGSVVQFKIKRHTP.SKLMK.YCE.QGLS.R...F.F..GQPIN
Retrocopy MAGGKPKEGIKTENNNHINLKVEGM<DGSVVQFKIKRHTPVSKLMKVYCE-QGLSKRRTKFDF<HGQPIN

Parental  ETDTPAQLEMEDEDTIDVFQQQTGGVF
          .T.T.AQL.MEDE.T.DVF..QTGGVF
Retrocopy DTNTTAQL*MEDENTTDVFLRQTGGVF

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_858 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 122 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009189	13 retrocopies	retro_amel_1097, retro_amel_1125, retro_amel_1199, retro_amel_1263, retro_amel_1434, retro_amel_152, retro_amel_1665, retro_amel_276, retro_amel_35, retro_amel_616, retro_amel_653, retro_amel_662, retro_amel_722,
Canis familiaris	ENSCAFG00000004724	1 retrocopy	retro_cfam_484,
Cavia porcellus	ENSCPOG00000004581	9 retrocopies	retro_cpor_1029, retro_cpor_1297, retro_cpor_1496, retro_cpor_202, retro_cpor_357, retro_cpor_823, retro_cpor_838, retro_cpor_869, retro_cpor_894,
Homo sapiens	ENSG00000188612	2 retrocopies	retro_hsap_4036, retro_hsap_4095,
Gorilla gorilla	ENSGGOG00000023769	3 retrocopies	retro_ggor_101, retro_ggor_184, retro_ggor_2576,
Loxodonta africana	ENSLAFG00000022855	5 retrocopies	retro_lafr_111, retro_lafr_1148, retro_lafr_189, retro_lafr_540, retro_lafr_951,
Loxodonta africana	ENSLAFG00000025811	10 retrocopies	retro_lafr_104, retro_lafr_1222, retro_lafr_1240, retro_lafr_200, retro_lafr_254, retro_lafr_324, retro_lafr_36, retro_lafr_488, retro_lafr_858 , retro_lafr_888,
Monodelphis domestica	ENSMODG00000007222	11 retrocopies	retro_mdom_1263, retro_mdom_1472, retro_mdom_1474, retro_mdom_1560, retro_mdom_1598, retro_mdom_1755, retro_mdom_237, retro_mdom_378, retro_mdom_517, retro_mdom_788, retro_mdom_986,
Mus musculus	ENSMUSG00000020738	19 retrocopies	retro_mmus_1498, retro_mmus_1772, retro_mmus_1903, retro_mmus_2050, retro_mmus_2323, retro_mmus_2475, retro_mmus_2492, retro_mmus_2590, retro_mmus_2767, retro_mmus_2917, retro_mmus_2974, retro_mmus_3209, retro_mmus_3414, retro_mmus_3630, retro_mmus_415, retro_mmus_611, retro_mmus_689, retro_mmus_818, retro_mmus_827,
Oryctolagus cuniculus	ENSOCUG00000028195	5 retrocopies	retro_ocun_110, retro_ocun_136, retro_ocun_175, retro_ocun_22, retro_ocun_46,
Pongo abelii	ENSPPYG00000029777	2 retrocopies	retro_pabe_164, retro_pabe_84,
Pan troglodytes	ENSPTRG00000042199	19 retrocopies	retro_ptro_1004, retro_ptro_1183, retro_ptro_1263, retro_ptro_135, retro_ptro_143, retro_ptro_1775, retro_ptro_2051, retro_ptro_2147, retro_ptro_2212, retro_ptro_2247, retro_ptro_2252, retro_ptro_2400, retro_ptro_2463, retro_ptro_2528, retro_ptro_2605, retro_ptro_2666, retro_ptro_2759, retro_ptro_3260, retro_ptro_65,
Sorex araneus	ENSSARG00000005720	8 retrocopies	retro_sara_156, retro_sara_158, retro_sara_175, retro_sara_389, retro_sara_70, retro_sara_717, retro_sara_749, retro_sara_93,
Sus scrofa	ENSSSCG00000017212	15 retrocopies	retro_sscr_1112, retro_sscr_1132, retro_sscr_1147, retro_sscr_1148, retro_sscr_123, retro_sscr_249, retro_sscr_277, retro_sscr_409, retro_sscr_591, retro_sscr_684, retro_sscr_754, retro_sscr_765, retro_sscr_814, retro_sscr_847, retro_sscr_969,