RetrogeneDB ID: retro_lafr_1196

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_87:5912254..5912833(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOA
• Ensembl ID: ENSLAFG00000009726
• Aliases: None
• Description: None

Sequence

>retro_lafr_1196
ATGGCTGCCATCGTGAAGAAATTGGTGATTGTTGGTGATGGACCTTGTGGCAAGACCTACTTGCTCAGAGTCTTCAGCAA
GGATCAGTTCCCCGAGGTGTATGTGCCCACAGTGTTTGAGAACTATGTGGCAGATATTGAAGTGTATGGAAAGCAGGTAG
AGTGGGCTTTGTGGGACACAGCTGGGCAAGAGGACTATGATCGTCTGAGGCCCCTCTCCTACCTGGACACTGATGTTATA
TTGATGTGTTTCTCCATCAACAGCCCTGATAGTTTAGAAAACATCCCAGAAAAATGGACCCCAGAAGTCAAGCATTTCTG
TCCCAATGTGCCCATCCTCCTGGTTGGGAACAAGAAGGATCTGCGGAATGATGAGCACACAAGGCGGGAGCTAGCCAAGA
TGAATCAGGAACCAGTATAACCTGAATAAGGCAGGGTTATGGGAAACAGGATTGGTGCTTTTGGGTACATGGAGTGTTCA
GCAAATACCAAAGAGGGAGTGAGGGAGGTTTTTGAAATGGCCACGAGAGCGGCTATGCAAGCCAGATGTGGGAATAAAAA
ATCTGGGTGCCTTGTCTTG

Alignment

ORF - retro_lafr_1196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
          MAAI.KKLVIVGDG.CGKT.LL.VFSKDQFPEVYVPTVFENYVADIEV.GKQVE.ALWDTAGQEDYDRLR
Retrocopy MAAIVKKLVIVGDGPCGKTYLLRVFSKDQFPEVYVPTVFENYVADIEVYGKQVEWALWDTAGQEDYDRLR

Parental  PLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVK
          PLSY.DTDVILMCFSI.SPDSLENIPEKWTPEVKHFCPNVPI.LVGNKKDLRNDEHTRRELAKM.QEPV.
Retrocopy PLSYLDTDVILMCFSINSPDSLENIPEKWTPEVKHFCPNVPILLVGNKKDLRNDEHTRRELAKMNQEPV*

Parental  PEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGCLVL
          PE.GR.M.NRIGAFGYMECSA.TK.GVREVFEMATRAA.QAR.G.KKSGCLVL
Retrocopy PE*GRVMGNRIGAFGYMECSANTKEGVREVFEMATRAAMQARCGNKKSGCLVL

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_1196 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 36 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008297	1 retrocopy	retro_acar_41,
Ailuropoda melanoleuca	ENSAMEG00000012584	3 retrocopies	retro_amel_101, retro_amel_1515, retro_amel_615,
Anas platyrhynchos	ENSAPLG00000014687	1 retrocopy	retro_apla_10,
Bos taurus	ENSBTAG00000004279	2 retrocopies	retro_btau_206, retro_btau_540,
Canis familiaris	ENSCAFG00000023066	2 retrocopies	retro_cfam_1652, retro_cfam_186,
Callithrix jacchus	ENSCJAG00000003904	3 retrocopies	retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Dasypus novemcinctus	ENSDNOG00000012825	6 retrocopies	retro_dnov_1012, retro_dnov_1814, retro_dnov_1904, retro_dnov_2090, retro_dnov_29, retro_dnov_326,
Dipodomys ordii	ENSDORG00000003382	3 retrocopies	retro_dord_1, retro_dord_18, retro_dord_538,
Felis catus	ENSFCAG00000027456	1 retrocopy	retro_fcat_29,
Gasterosteus aculeatus	ENSGACG00000005670	1 retrocopy	retro_gacu_9,
Gallus gallus	ENSGALG00000003806	1 retrocopy	retro_ggal_5,
Gorilla gorilla	ENSGGOG00000012843	1 retrocopy	retro_ggor_2450,
Gadus morhua	ENSGMOG00000008188	1 retrocopy	retro_gmor_18,
Latimeria chalumnae	ENSLACG00000016941	1 retrocopy	retro_lcha_15,
Loxodonta africana	ENSLAFG00000009726	8 retrocopies	retro_lafr_1196 , retro_lafr_1197, retro_lafr_1198, retro_lafr_178, retro_lafr_203, retro_lafr_261, retro_lafr_392, retro_lafr_82,
Meleagris gallopavo	ENSMGAG00000002280	1 retrocopy	retro_mgal_2,
Myotis lucifugus	ENSMLUG00000013911	6 retrocopies	retro_mluc_108, retro_mluc_193, retro_mluc_1976, retro_mluc_2553, retro_mluc_2554, retro_mluc_2555,
Macaca mulatta	ENSMMUG00000012962	1 retrocopy	retro_mmul_977,
Monodelphis domestica	ENSMODG00000012981	2 retrocopies	retro_mdom_19, retro_mdom_294,
Mus musculus	ENSMUSG00000007815	9 retrocopies	retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,
Nomascus leucogenys	ENSNLEG00000006839	4 retrocopies	retro_nleu_104, retro_nleu_2207, retro_nleu_377, retro_nleu_814,
Ornithorhynchus anatinus	ENSOANG00000013807	1 retrocopy	retro_oana_7,
Oryctolagus cuniculus	ENSOCUG00000013323	3 retrocopies	retro_ocun_1075, retro_ocun_726, retro_ocun_854,
Otolemur garnettii	ENSOGAG00000028489	1 retrocopy	retro_ogar_2340,
Oreochromis niloticus	ENSONIG00000018884	1 retrocopy	retro_onil_32,
Procavia capensis	ENSPCAG00000009699	3 retrocopies	retro_pcap_191, retro_pcap_202, retro_pcap_98,
Pelodiscus sinensis	ENSPSIG00000015328	1 retrocopy	retro_psin_7,
Pan troglodytes	ENSPTRG00000014922	3 retrocopies	retro_ptro_10, retro_ptro_2456, retro_ptro_625,
Pteropus vampyrus	ENSPVAG00000008738	1 retrocopy	retro_pvam_599,
Rattus norvegicus	ENSRNOG00000050519	3 retrocopies	retro_rnor_127, retro_rnor_2899, retro_rnor_408,
Sarcophilus harrisii	ENSSHAG00000016308	2 retrocopies	retro_shar_60, retro_shar_96,
Sus scrofa	ENSSSCG00000022080	1 retrocopy	retro_sscr_72,
Ictidomys tridecemlineatus	ENSSTOG00000004561	2 retrocopies	retro_itri_39, retro_itri_96,
Takifugu rubripes	ENSTRUG00000011944	1 retrocopy	retro_trub_19,
Tarsius syrichta	ENSTSYG00000008220	3 retrocopies	retro_tsyr_1604, retro_tsyr_413, retro_tsyr_593,
Vicugna pacos	ENSVPAG00000010931	3 retrocopies	retro_vpac_130, retro_vpac_24, retro_vpac_492,