RetrogeneDB ID: retro_lafr_287

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_11:27433561..27433870(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC15
• Ensembl ID: ENSLAFG00000004343
• Aliases: None
• Description: None

Sequence

>retro_lafr_287
GTGATAGCCTTTGCATTTGCGGGTCGCTATGCATTTCAGACCTGGAAACCTCTAGAACAAGTAACCACAGAAACTGCAAA
GAAGATTGCAAATCCTAGCTTTTCATCTGACTGTAAAGGAGGATTTGAACAGAAAATGAGTAGGTGAGAAGCTAGTCTGA
TTTTAGGTGTAATCCCACCTTCGGGCAAGGACAAGATTAGTACACCCCACAGGAGAATCATGATTTTGAACCGCCCAGAT
AAAGATGGCTCTCCTTACCCACCAACTAAAATAATTGAAGCAAAAGACTTGCTAGAATCAAGCATCAAA

Alignment

ORF - retro_lafr_287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.61 %
• Parental protein coverage: 70.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAAFAFAGRYAFQIWKPLEQVITETAKKISNPSLSSYYKGGFEQKMSRREASLILGVSPSADKAKIRTAH
          V.AFAFAGRYAFQ.WKPLEQV.TETAKKI.NPS.SS..KGGFEQKMSR.EASLILGV.P...K.KI.T.H
Retrocopy VIAFAFAGRYAFQTWKPLEQVTTETAKKIANPSFSSDCKGGFEQKMSR*EASLILGVIPPSGKDKISTPH

Parental  RRIMILNHPDKGGSPYLATKINEAKDLLESSTK
          RRIMILN.PDK.GSPY..TKI.EAKDLLESS.K
Retrocopy RRIMILNRPDKDGSPYPPTKIIEAKDLLESSIK

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_287 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 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034785	1 retrocopy	retro_btau_1624,
Canis familiaris	ENSCAFG00000004664	1 retrocopy	retro_cfam_939,
Callithrix jacchus	ENSCJAG00000017589	2 retrocopies	retro_cjac_1663, retro_cjac_634,
Cavia porcellus	ENSCPOG00000003485	1 retrocopy	retro_cpor_327,
Equus caballus	ENSECAG00000007757	1 retrocopy	retro_ecab_561,
Erinaceus europaeus	ENSEEUG00000008785	5 retrocopies	retro_eeur_360, retro_eeur_608, retro_eeur_64, retro_eeur_93, retro_eeur_95,
Felis catus	ENSFCAG00000022632	1 retrocopy	retro_fcat_259,
Homo sapiens	ENSG00000120675	2 retrocopies	retro_hsap_3331, retro_hsap_4312,
Gorilla gorilla	ENSGGOG00000016338	2 retrocopies	retro_ggor_1294, retro_ggor_2882,
Loxodonta africana	ENSLAFG00000001910	5 retrocopies	retro_lafr_48, retro_lafr_515, retro_lafr_611, retro_lafr_881, retro_lafr_929,
Loxodonta africana	ENSLAFG00000004343	2 retrocopies	retro_lafr_287 , retro_lafr_942,
Myotis lucifugus	ENSMLUG00000008684	3 retrocopies	retro_mluc_1358, retro_mluc_1544, retro_mluc_520,
Macaca mulatta	ENSMMUG00000013689	1 retrocopy	retro_mmul_1169,
Mustela putorius furo	ENSMPUG00000001704	1 retrocopy	retro_mputfur_1065,
Nomascus leucogenys	ENSNLEG00000001759	4 retrocopies	retro_nleu_1408, retro_nleu_1464, retro_nleu_1675, retro_nleu_585,
Oryctolagus cuniculus	ENSOCUG00000001696	4 retrocopies	retro_ocun_1101, retro_ocun_487, retro_ocun_882, retro_ocun_936,
Ochotona princeps	ENSOPRG00000016191	5 retrocopies	retro_opri_1038, retro_opri_235, retro_opri_285, retro_opri_756, retro_opri_766,
Pongo abelii	ENSPPYG00000005323	1 retrocopy	retro_pabe_3508,
Pan troglodytes	ENSPTRG00000005831	2 retrocopies	retro_ptro_2148, retro_ptro_2920,
Pteropus vampyrus	ENSPVAG00000011281	1 retrocopy	retro_pvam_807,
Sorex araneus	ENSSARG00000007683	1 retrocopy	retro_sara_658,
Ictidomys tridecemlineatus	ENSSTOG00000012805	1 retrocopy	retro_itri_1710,
Taeniopygia guttata	ENSTGUG00000012364	2 retrocopies	retro_tgut_20, retro_tgut_45,
Tursiops truncatus	ENSTTRG00000015580	1 retrocopy	retro_ttru_1021,
Vicugna pacos	ENSVPAG00000001445	1 retrocopy	retro_vpac_113,