RetrogeneDB ID: retro_lafr_610

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_25:12223311..12223662(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000028465
• Aliases: None
• Description: None

Sequence

>retro_lafr_610
GAAGACAGCTCTGTTGCAGCCAGGTTTCAACACATGAGGGAGGAATTTGATAGAATTGTAATACGGAAAACTGGAGAAGG
AGTTCTGATTGTACATGACCACTGGTTACCCCATGTATTACTGCTACAGCTGGGAGCAAGTTTCTTCAGATTACCTGGAG
GTGAACTTAATCCAGGAGAAGATGAAGTTGAAGGAATAAAATGCTTAATGACAGAGGTACTAGTTTGTTAAGATGGAGTC
CTGCAAGATTGGGTCATTGATGACTGGATTGCTAACTGGTGGAGACCAAATTTTGAACCACCTCTGTATCCACATGTTCC
TGCACTTACCTCAAAGCCTAAGGAATGTAAA

Alignment

ORF - retro_lafr_610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 51.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLM
          .DSSVAARFQ.MREEFD.I..R.T.EGVLIVH.H.LPHVLLLQLG..FF.LPGGELNPGEDEVEG.K.LM
Retrocopy EDSSVAARFQHMREEFDRIVIRKTGEGVLIVHDHWLPHVLLLQLGASFFRLPGGELNPGEDEVEGIKCLM

Parental  TEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHK
          TE.L...DGVLQDWVIDD.I.NWWRPNFEPP.YP..PA...KPKE.K
Retrocopy TEVLVC*DGVLQDWVIDDWIANWWRPNFEPPLYPHVPALTSKPKECK

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_610 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 25 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016628	1 retrocopy	retro_amel_540,
Bos taurus	ENSBTAG00000010207	2 retrocopies	retro_btau_1655, retro_btau_937,
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Cavia porcellus	ENSCPOG00000003705	1 retrocopy	retro_cpor_1054,
Equus caballus	ENSECAG00000001043	1 retrocopy	retro_ecab_292,
Erinaceus europaeus	ENSEEUG00000003402	1 retrocopy	retro_eeur_35,
Echinops telfairi	ENSETEG00000013634	1 retrocopy	retro_etel_622,
Felis catus	ENSFCAG00000008669	1 retrocopy	retro_fcat_1843,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610 ,
Myotis lucifugus	ENSMLUG00000004968	2 retrocopies	retro_mluc_1576, retro_mluc_999,
Macaca mulatta	ENSMMUG00000019906	1 retrocopy	retro_mmul_1360,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Mus musculus	ENSMUSG00000031754	3 retrocopies	retro_mmus_1949, retro_mmus_1950, retro_mmus_2142,
Nomascus leucogenys	ENSNLEG00000001963	2 retrocopies	retro_nleu_1477, retro_nleu_2493,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Otolemur garnettii	ENSOGAG00000014888	2 retrocopies	retro_ogar_1450, retro_ogar_630,
Ochotona princeps	ENSOPRG00000006689	1 retrocopy	retro_opri_637,
Pteropus vampyrus	ENSPVAG00000014583	2 retrocopies	retro_pvam_533, retro_pvam_711,
Sorex araneus	ENSSARG00000006493	2 retrocopies	retro_sara_161, retro_sara_580,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tupaia belangeri	ENSTBEG00000007664	1 retrocopy	retro_tbel_4003,
Tarsius syrichta	ENSTSYG00000014602	4 retrocopies	retro_tsyr_1685, retro_tsyr_1888, retro_tsyr_790, retro_tsyr_988,
Tursiops truncatus	ENSTTRG00000013545	1 retrocopy	retro_ttru_1087,
Vicugna pacos	ENSVPAG00000003701	2 retrocopies	retro_vpac_340, retro_vpac_605,