RetrogeneDB ID: retro_lafr_540

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_20:37617809..37618089(+)
• Located in intron of: ENSLAFG00000014458

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSLAFG00000022855
• Aliases: None
• Description: None

Sequence

>retro_lafr_540
CAAGACCTTCAGCCGAGGACCGAGGACTTGGGTAATAACAACAAAGGAGACTATTTCAAACTCAAAGTCCCTGGGCAGGA
CAGCAGTGAGATTCACTCCAAGGTGAAAATGGCCAACACACCTCAAGAAACTCAGACTCACACCGTCAAAGATGCAAAGC
TCTAGTGAACTCACTCCAATGAGAGGGTTTCTCTTTGAAAGCTGGAGAACAGCTGATAATCACCCTCCAAAAGAATTGGG
CATAGAGGAAGAAGATGTGACTGAAGTCTGTCGGGATAAA

Alignment

ORF - retro_lafr_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.21 %
• Parental protein coverage: 90.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMT-THLKKLKESYCQRQG----VPMNSLRFLFEG
          Q...P.TEDLG....G.Y.KLKV.GQDSSEIH.KVKM..THLKKL.......Q......PM....F..E.
Retrocopy QDLQPRTEDLGNNNKGDYFKLKVPGQDSSEIHSKVKMA>THLKKLRLTPSKMQSSSELTPMRGFLF--ES

Parental  QRIADNHTPKELGMEEEDVIEVYQEQ
          .R.ADNH.PKELG.EEEDV.EV....
Retrocopy WRTADNHPPKELGIEEEDVTEVCRDK

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_540 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 17 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013225	5 retrocopies	retro_amel_1068, retro_amel_233, retro_amel_236, retro_amel_315, retro_amel_49,
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Choloepus hoffmanni	ENSCHOG00000009739	2 retrocopies	retro_chof_190, retro_chof_2068,
Dasypus novemcinctus	ENSDNOG00000015868	10 retrocopies	retro_dnov_1070, retro_dnov_1324, retro_dnov_1610, retro_dnov_1623, retro_dnov_1826, retro_dnov_1876, retro_dnov_2068, retro_dnov_2330, retro_dnov_2423, retro_dnov_997,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Loxodonta africana	ENSLAFG00000022855	5 retrocopies	retro_lafr_111, retro_lafr_1148, retro_lafr_189, retro_lafr_540 , retro_lafr_951,
Loxodonta africana	ENSLAFG00000025811	10 retrocopies	retro_lafr_104, retro_lafr_1222, retro_lafr_1240, retro_lafr_200, retro_lafr_254, retro_lafr_324, retro_lafr_36, retro_lafr_488, retro_lafr_858, retro_lafr_888,
Microcebus murinus	ENSMICG00000008968	5 retrocopies	retro_mmur_1177, retro_mmur_1300, retro_mmur_1493, retro_mmur_1554, retro_mmur_1602,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Macaca mulatta	ENSMMUG00000005240	7 retrocopies	retro_mmul_1108, retro_mmul_2035, retro_mmul_2081, retro_mmul_313, retro_mmul_373, retro_mmul_450, retro_mmul_855,
Nomascus leucogenys	ENSNLEG00000006997	4 retrocopies	retro_nleu_277, retro_nleu_384, retro_nleu_855, retro_nleu_865,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Procavia capensis	ENSPCAG00000006870	1 retrocopy	retro_pcap_136,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,