RetrogeneDB ID: retro_lafr_458

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_17:5188606..5189035(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCNP
• Ensembl ID: ENSLAFG00000005518
• Aliases: None
• Description: None

Sequence

>retro_lafr_458
ATCCGTCAGAGTAATGGAGGGGAAATTTCGGGTCACAGCGCTGAGAAACAATCAGCTGAAGAAGAAGCTGGAGATTTCCC
AAACAAAGCCTACAAAGATCTCCAAGTTTGGATTTGCCATAGGTAGTCAGATGACAAAGAAAGCATCAGCCATATCCATC
AAACTTGGATCAAGTAAGCCTTAAGAAACAGTTCCAACTCTTGCTCCGAAAACCTTTCAATAGCAGCAGCTTTTAATGAA
GACGAAGGTAGTGAACCAGAGGAAATGCCTCCAGAAGCAAAGTTGAGGATGAAGAAAATTGGAATGGATACACCAACATC
AGCAGGACCAAACTCCTTCAACAAAGGAAAGCATGGGTTTTCGGATAACCAGAAGCTATGGGAGTGAAATATAAAATCTC
ATCTTGGAAATGTCCATGACCAATACAAT

Alignment

ORF - retro_lafr_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.59 %
• Parental protein coverage: 80.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSSSNGGESSSRSAEKRSAEEEAGDFP-TKPTKISKFGFAIGSQTTKKASAISIKLGSSKPKETVPTLAP
          ...SNGGE.S..SAEK.SAEEEAGDFP.TKPTKISKFGFAIGSQ.TKKASAISIKLGSSKP.ETVPTLAP
Retrocopy IRQSNGGEISGHSAEKQSAEEEAGDFP>TKPTKISKFGFAIGSQMTKKASAISIKLGSSKP*ETVPTLAP

Parental  KT-LSVAAAFNEDEDSEPEEMPPEAKMRMKNIGRDTPTSAGPNSFNKGKHGFSDNQKLWERNIKSHLGNV
          KT.LS.AAAFNEDE.SEPEEMPPEAK.RMK.IG.DTPTSAGPNSFNKGKHGFSDNQKLWE.NIKSHLGNV
Retrocopy KT<LSIAAAFNEDEGSEPEEMPPEAKLRMKKIGMDTPTSAGPNSFNKGKHGFSDNQKLWE*NIKSHLGNV

Parental  HDQDN
          HDQ.N
Retrocopy HDQYN

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_458 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 27 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003777	2 retrocopies	retro_amel_1086, retro_amel_1679,
Canis familiaris	ENSCAFG00000009593	3 retrocopies	retro_cfam_1850, retro_cfam_2074, retro_cfam_2160,
Choloepus hoffmanni	ENSCHOG00000007972	11 retrocopies	retro_chof_1170, retro_chof_1215, retro_chof_2070, retro_chof_2280, retro_chof_2290, retro_chof_2553, retro_chof_2575, retro_chof_594, retro_chof_651, retro_chof_806, retro_chof_819,
Callithrix jacchus	ENSCJAG00000000508	6 retrocopies	retro_cjac_101, retro_cjac_1569, retro_cjac_1722, retro_cjac_3205, retro_cjac_3332, retro_cjac_401,
Cavia porcellus	ENSCPOG00000010610	2 retrocopies	retro_cpor_1335, retro_cpor_443,
Dasypus novemcinctus	ENSDNOG00000008873	5 retrocopies	retro_dnov_1606, retro_dnov_259, retro_dnov_370, retro_dnov_910, retro_dnov_98,
Felis catus	ENSFCAG00000029026	2 retrocopies	retro_fcat_1767, retro_fcat_1822,
Homo sapiens	ENSG00000081154	3 retrocopies	retro_hsap_1130, retro_hsap_1155, retro_hsap_1264,
Gorilla gorilla	ENSGGOG00000025423	4 retrocopies	retro_ggor_882, retro_ggor_901, retro_ggor_902, retro_ggor_994,
Loxodonta africana	ENSLAFG00000005518	2 retrocopies	retro_lafr_1189, retro_lafr_458 ,
Microcebus murinus	ENSMICG00000008072	10 retrocopies	retro_mmur_1010, retro_mmur_1138, retro_mmur_1286, retro_mmur_148, retro_mmur_1535, retro_mmur_1547, retro_mmur_1625, retro_mmur_167, retro_mmur_458, retro_mmur_887,
Myotis lucifugus	ENSMLUG00000005878	5 retrocopies	retro_mluc_1010, retro_mluc_1818, retro_mluc_2423, retro_mluc_603, retro_mluc_816,
Macaca mulatta	ENSMMUG00000017782	3 retrocopies	retro_mmul_1312, retro_mmul_1377, retro_mmul_2598,
Mustela putorius furo	ENSMPUG00000011696	1 retrocopy	retro_mputfur_850,
Mus musculus	ENSMUSG00000071533	4 retrocopies	retro_mmus_2331, retro_mmus_2339, retro_mmus_2822, retro_mmus_3034,
Nomascus leucogenys	ENSNLEG00000003224	2 retrocopies	retro_nleu_2100, retro_nleu_2971,
Oryctolagus cuniculus	ENSOCUG00000011110	7 retrocopies	retro_ocun_1072, retro_ocun_1144, retro_ocun_1496, retro_ocun_1537, retro_ocun_573, retro_ocun_687, retro_ocun_868,
Otolemur garnettii	ENSOGAG00000001821	4 retrocopies	retro_ogar_2216, retro_ogar_2465, retro_ogar_3320, retro_ogar_652,
Procavia capensis	ENSPCAG00000007007	3 retrocopies	retro_pcap_161, retro_pcap_194, retro_pcap_273,
Pongo abelii	ENSPPYG00000013591	5 retrocopies	retro_pabe_1051, retro_pabe_1598, retro_pabe_3778, retro_pabe_935, retro_pabe_961,
Pan troglodytes	ENSPTRG00000015172	3 retrocopies	retro_ptro_676, retro_ptro_790, retro_ptro_864,
Pteropus vampyrus	ENSPVAG00000009886	2 retrocopies	retro_pvam_1277, retro_pvam_421,
Rattus norvegicus	ENSRNOG00000028411	1 retrocopy	retro_rnor_2138,
Sorex araneus	ENSSARG00000001433	2 retrocopies	retro_sara_265, retro_sara_626,
Sus scrofa	ENSSSCG00000011955	5 retrocopies	retro_sscr_1030, retro_sscr_1124, retro_sscr_451, retro_sscr_696, retro_sscr_728,
Tursiops truncatus	ENSTTRG00000015008	1 retrocopy	retro_ttru_1167,
Vicugna pacos	ENSVPAG00000012239	1 retrocopy	retro_vpac_564,