RetrogeneDB ID: retro_lafr_437

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_16:17788354..17788766(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HRSP12
• Ensembl ID: ENSLAFG00000002078
• Aliases: None
• Description: None

Sequence

>retro_lafr_437
ATGTCGTCCTTGATTCGAAAGGTGATCAGTACCGCGAAAGCCCCAGCAGCCATTGGTCCCTACAGTCAAGCTGTGCTAAT
CGACAGGAGAGTTTACATTTCGGAACAGATAGGTATGGACCCTTCAAGTGGACAGCTTGTGCCAGGAGGGGTGGTAGGAG
AAACTAAACAAGCTCTTACAAATACTGGTGAAGTTCTGAAAGCCTCAGGCTGTGACTACACTAATGTGGTGAAAACAACT
GTGCTGCTGGCTGACATAAATTGACTTCGCTGCTGTCAATGAAATCTACCAACAGTTTTTCAAGAGTAATTTTCCTGCTA
GAGCTGCTTACCAAGTTGCTGCTTTGCCCAAAGGAAGCTGTATTGAGATTGAGGCAATAGCTGTCCAAGGACCACTCTCA
CCAGCATTACTA

Alignment

ORF - retro_lafr_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSLIRKVISTAKAPAAIGPYSQAVLIDRTVYISGQIGMDPSSGQLVPGGVVGETKQALTNIGEVLKAAG
          MSSLIRKVISTAKAPAAIGPYSQAVLIDR.VYIS.QIGMDPSSGQLVPGGVVGETKQALTN.GEVLKA.G
Retrocopy MSSLIRKVISTAKAPAAIGPYSQAVLIDRRVYISEQIGMDPSSGQLVPGGVVGETKQALTNTGEVLKASG

Parental  CDYSNVVKTTVLLADIN-DFTAVNEIYQQFFKSNFPARAAYQVAALPKGSRVEIEAIAVQGPLSPALL
          CDY.NVVKTTVLLADIN.DF.AVNEIYQQFFKSNFPARAAYQVAALPKGS..EIEAIAVQGPLSPALL
Retrocopy CDYTNVVKTTVLLADIN>DFAAVNEIYQQFFKSNFPARAAYQVAALPKGSCIEIEAIAVQGPLSPALL

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_437 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 28 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000575	1 retrocopy	retro_amel_1033,
Bos taurus	ENSBTAG00000012595	5 retrocopies	retro_btau_1068, retro_btau_1145, retro_btau_1328, retro_btau_771, retro_btau_912,
Canis familiaris	ENSCAFG00000030250	1 retrocopy	retro_cfam_668,
Choloepus hoffmanni	ENSCHOG00000001278	8 retrocopies	retro_chof_133, retro_chof_1972, retro_chof_2434, retro_chof_2503, retro_chof_2676, retro_chof_380, retro_chof_515, retro_chof_757,
Callithrix jacchus	ENSCJAG00000015560	2 retrocopies	retro_cjac_1702, retro_cjac_465,
Dasypus novemcinctus	ENSDNOG00000025138	3 retrocopies	retro_dnov_1155, retro_dnov_224, retro_dnov_793,
Dipodomys ordii	ENSDORG00000015382	2 retrocopies	retro_dord_576, retro_dord_713,
Erinaceus europaeus	ENSEEUG00000014805	1 retrocopy	retro_eeur_256,
Felis catus	ENSFCAG00000002167	1 retrocopy	retro_fcat_624,
Homo sapiens	ENSG00000132541	3 retrocopies	retro_hsap_1502, retro_hsap_284, retro_hsap_3022,
Gorilla gorilla	ENSGGOG00000001185	1 retrocopy	retro_ggor_1153,
Loxodonta africana	ENSLAFG00000002078	1 retrocopy	retro_lafr_437 ,
Microcebus murinus	ENSMICG00000004356	13 retrocopies	retro_mmur_1096, retro_mmur_1206, retro_mmur_1323, retro_mmur_209, retro_mmur_222, retro_mmur_364, retro_mmur_533, retro_mmur_589, retro_mmur_597, retro_mmur_603, retro_mmur_79, retro_mmur_870, retro_mmur_97,
Macaca mulatta	ENSMMUG00000011825	2 retrocopies	retro_mmul_558, retro_mmul_88,
Monodelphis domestica	ENSMODG00000006575	1 retrocopy	retro_mdom_319,
Mustela putorius furo	ENSMPUG00000015253	1 retrocopy	retro_mputfur_1449,
Mus musculus	ENSMUSG00000022323	1 retrocopy	retro_mmus_3584,
Nomascus leucogenys	ENSNLEG00000002485	3 retrocopies	retro_nleu_1721, retro_nleu_3065, retro_nleu_837,
Ornithorhynchus anatinus	ENSOANG00000021532	1 retrocopy	retro_oana_33,
Otolemur garnettii	ENSOGAG00000001465	3 retrocopies	retro_ogar_2308, retro_ogar_2951, retro_ogar_552,
Pongo abelii	ENSPPYG00000018776	3 retrocopies	retro_pabe_1253, retro_pabe_2504, retro_pabe_387,
Pan troglodytes	ENSPTRG00000020457	3 retrocopies	retro_ptro_1019, retro_ptro_2040, retro_ptro_234,
Sus scrofa	ENSSSCG00000006079	1 retrocopy	retro_sscr_834,
Ictidomys tridecemlineatus	ENSSTOG00000011452	4 retrocopies	retro_itri_1591, retro_itri_192, retro_itri_605, retro_itri_894,
Tupaia belangeri	ENSTBEG00000002602	10 retrocopies	retro_tbel_1543, retro_tbel_1602, retro_tbel_2450, retro_tbel_2868, retro_tbel_2995, retro_tbel_3589, retro_tbel_421, retro_tbel_621, retro_tbel_888, retro_tbel_953,
Tarsius syrichta	ENSTSYG00000003085	6 retrocopies	retro_tsyr_120, retro_tsyr_1541, retro_tsyr_226, retro_tsyr_373, retro_tsyr_624, retro_tsyr_798,
Tursiops truncatus	ENSTTRG00000016066	5 retrocopies	retro_ttru_1282, retro_ttru_1589, retro_ttru_1626, retro_ttru_369, retro_ttru_909,
Vicugna pacos	ENSVPAG00000008277	3 retrocopies	retro_vpac_30, retro_vpac_358, retro_vpac_89,