RetrogeneDB ID: retro_lafr_959

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_51:15108290..15108695(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3A
• Ensembl ID: ENSLAFG00000008083
• Aliases: None
• Description: Histone H3 [Source:UniProtKB/TrEMBL;Acc:G3T157]

Sequence

>retro_lafr_959
TTGGCTCGTACAAAGCAGACTCCCAAACCAACCAGTTGTCAAGCACCCAGGAAGCAACTGGCCACAAAAGCTGCTCTCAA
GGATGTATCTTCTACTGCAGGGCTGAAGAAGCCTCATCATTACAGGCCTGGTACTGTGGCACTCCGGGAAATCAGAAGTT
ATCAGAAGTCTCCTGAACTTCTGACTTGCACATTTCCCTTCCAGCATCTGGTATGAGAAATTGCTCAGGACTTCAAAACA
GATCTGCATTTCCAGGGTGCAGCTACTGGTGCTTTGCAGGCGGCAAGTGAGGCCTACCTGTTTGGCCTTTTTGAAGACAC
CAACCTGTGTGCTATGCATGCCAAACATGTAACAATTGTGCCAAAAGACATCTAGCTAGCACATCGCATATGTGGAGAAC
GTGCT

Alignment

ORF - retro_lafr_959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          .ARTKQT..K.T...APRKQLATKAA.K...ST.G.KKPH.YRPGTVALREIR.YQKS.ELL....PFQ.
Retrocopy LARTKQTP-KPTSCQAPRKQLATKAALKDVSSTAGLKKPHHYRPGTVALREIRSYQKSPELLTCTFPFQH

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LV.EIAQDFKTDL.FQ.AA.GALQ.ASEAYL.GLFEDTNLCA.HAK.VTI.PKDI.LA.RI.GERA
Retrocopy LV*EIAQDFKTDLHFQGAATGALQAASEAYLFGLFEDTNLCAMHAKHVTIVPKDI*LAHRICGERA

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_959 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 12 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Dasypus novemcinctus	ENSDNOG00000024843	2 retrocopies	retro_dnov_1624, retro_dnov_775,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266,
Homo sapiens	ENSG00000132475	11 retrocopies	retro_hsap_1212, retro_hsap_1552, retro_hsap_2180, retro_hsap_24, retro_hsap_2971, retro_hsap_3231, retro_hsap_3294, retro_hsap_3299, retro_hsap_389, retro_hsap_4236, retro_hsap_911,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104,
Loxodonta africana	ENSLAFG00000008083	3 retrocopies	retro_lafr_837, retro_lafr_959 , retro_lafr_99,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Mustela putorius furo	ENSMPUG00000004555	4 retrocopies	retro_mputfur_389, retro_mputfur_82, retro_mputfur_99, retro_mputfur_990,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,