RetrogeneDB ID: retro_lafr_500

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:17449546..17450019(+)
• Located in intron of: ENSLAFG00000010490

Retrocopy information

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

Parental gene information

• Parental gene symbol: MKI67IP
• Ensembl ID: ENSLAFG00000030731
• Aliases: None
• Description: None

Sequence

>retro_lafr_500
AAAGGTGATTTTATGCCACCTGAAAAGGTACATGAAAAAGTTTTCAAAGACTGGGATGTTCCATTTTCAAAGCCATCATA
TCCAGCAGTAAAACGGTACAATAAGAAACGGTCACTTACACAGAAGATACGGATGGAGAAGCGATTTAAAAACAAAGAAA
AATTACTTAGGAAAGAGTTAGCTAAAAAAGGAATAGTGTGTAATTTTCCAGCATTGATTTTACCAAAGAAGAAAAAAGGA
AATGTTTCAAACACAGATCTTCAGAACTCTACAAATAGCCAGGGCTCCACACCAGTTTGTATATCAACATTTTTGGAGAG
GCGAAAAATGTGAAGTGGCTGAAATAAATGATGATGAGGAAGATAACGAAATCATTTTCAAACAGCCTGTGCTGGGTGTA
AAAGAAGAAACCCAAGAGACTCAAACATCTACCCGTTCAGGGAAAAAAAAGACGACGACGAAAAAGCAAACAG

Alignment

ORF - retro_lafr_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 57.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KCDFMPPEKVHEKVFKDWDVPFSKPSYPAVKRYNKKRSLTQKLRMEKRFKNKEKLLRKKLAKKGIVYNFP
          K.DFMPPEKVHEKVFKDWDVPFSKPSYPAVKRYNKKRSLTQK.RMEKRFKNKEKLLRK.LAKKGIV.NFP
Retrocopy KGDFMPPEKVHEKVFKDWDVPFSKPSYPAVKRYNKKRSLTQKIRMEKRFKNKEKLLRKELAKKGIVCNFP

Parental  SLILPKKKKGNVSNTDLQSSTNSQGSTPVCTPTFLERR-KCEVAEMNDDEEDKEIIFKQPVAGVKEEAQE
          .LILPKKKKGNVSNTDLQ.STNSQGSTPVC..TFLERR.KCEVAE.NDDEED.EIIFKQPV.GVKEE.QE
Retrocopy ALILPKKKKGNVSNTDLQNSTNSQGSTPVCISTFLERR>KCEVAEINDDEEDNEIIFKQPVLGVKEETQE

Parental  TQTSTRS-GKKRQRRRKSKQ
          TQTSTRS.GKKR.R.RKSKQ
Retrocopy TQTSTRS>GKKRRR-RKSKQ

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_500 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 19 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019387	1 retrocopy	retro_btau_1516,
Choloepus hoffmanni	ENSCHOG00000002227	5 retrocopies	retro_chof_1061, retro_chof_1449, retro_chof_1735, retro_chof_236, retro_chof_2480,
Callithrix jacchus	ENSCJAG00000013386	1 retrocopy	retro_cjac_3076,
Dasypus novemcinctus	ENSDNOG00000005017	2 retrocopies	retro_dnov_1869, retro_dnov_2487,
Erinaceus europaeus	ENSEEUG00000008535	3 retrocopies	retro_eeur_530, retro_eeur_550, retro_eeur_91,
Homo sapiens	ENSG00000155438	5 retrocopies	retro_hsap_1077, retro_hsap_1596, retro_hsap_1609, retro_hsap_1611, retro_hsap_553,
Gorilla gorilla	ENSGGOG00000023498	4 retrocopies	retro_ggor_1213, retro_ggor_1923, retro_ggor_2225, retro_ggor_850,
Loxodonta africana	ENSLAFG00000030731	1 retrocopy	retro_lafr_500 ,
Microcebus murinus	ENSMICG00000015787	1 retrocopy	retro_mmur_990,
Myotis lucifugus	ENSMLUG00000006481	2 retrocopies	retro_mluc_1217, retro_mluc_1369,
Macaca mulatta	ENSMMUG00000020928	11 retrocopies	retro_mmul_1444, retro_mmul_1544, retro_mmul_2149, retro_mmul_2151, retro_mmul_2225, retro_mmul_2226, retro_mmul_2389, retro_mmul_690, retro_mmul_696, retro_mmul_697, retro_mmul_752,
Monodelphis domestica	ENSMODG00000000152	2 retrocopies	retro_mdom_1271, retro_mdom_737,
Nomascus leucogenys	ENSNLEG00000001163	4 retrocopies	retro_nleu_1756, retro_nleu_1942, retro_nleu_2022, retro_nleu_669,
Pongo abelii	ENSPPYG00000025875	2 retrocopies	retro_pabe_2248, retro_pabe_510,
Pan troglodytes	ENSPTRG00000012419	5 retrocopies	retro_ptro_1072, retro_ptro_1077, retro_ptro_1080, retro_ptro_1378, retro_ptro_415,
Pteropus vampyrus	ENSPVAG00000016707	1 retrocopy	retro_pvam_134,
Sorex araneus	ENSSARG00000006252	1 retrocopy	retro_sara_362,
Tupaia belangeri	ENSTBEG00000001123	4 retrocopies	retro_tbel_1731, retro_tbel_3479, retro_tbel_4589, retro_tbel_926,
Vicugna pacos	ENSVPAG00000005847	2 retrocopies	retro_vpac_136, retro_vpac_265,