RetrogeneDB ID: retro_lafr_1079

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_66:11120873..11121363(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM204A
• Ensembl ID: ENSLAFG00000016774
• Aliases: None
• Description: None

Sequence

>retro_lafr_1079
ATGTGGCGTGAGCTGCTACCTCTTGGCCTAAATGAAAGTGATGTTGAGTTAAATTCTGAAGATGAAGCCGTATCAGAAAG
CTCTGGACTTCACTTACAGGAAGCTAAAGATGAGATGACTAGAGAAACAGAAATCTCAGATTTCCCGAGAGACAGACCAA
AAACCGAAACAGAGCCAAATGCAAATGCCTATACAGAGTACCCTTCCAGAACTTCCTTACACATGCGGGATAAATCTCAG
TAACTGCATAAAAATCATTCTGAACTGCAAACCTCAACCTCGAGATTCAGGAGGAAAAAAGGAAATGCTCCAGGAAAGGT
AAATTGAAGCAAGAAGCGACACCTCGTAGTGAACATCCTCTAACGAAACCCAGCGGAAGGCGCTTACTCAGTATTTTGGA
GTCGGTTCAATCCCCTGTAAAAAAGGAATCAACGACAAGTCAGGTCTTGAAAAAAGCATAGCCCAGGCTGTGCAAGAATG
GGATATTGAG

Alignment

ORF - retro_lafr_1079 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.41 %
• Parental protein coverage: 72.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MWSGLLPPGLNESDVELSSEDEAKSENSGLHLLEAEEDQMTRKTEISDFPTDGPKTETEANTNAYEECPS
          MW..LLP.GLNESDVEL.SEDEA.SE.SGLHL.EA..D.MTR.TEISDFP.D.PKTETE.N.NAY.E.PS
Retrocopy MWRELLPLGLNESDVELNSEDEAVSESSGLHLQEAK-DEMTRETEISDFPRDRPKTETEPNANAYTEYPS

Parental  GISLHTWNRFQELHKKHSEQKTSASRFRRK-KRKRSRKGKLKNEETSCSEQ-SSNETQWKELTQYFGVND
          ..SLH.....Q.LHK.HSE..TS.SRFRRK.KRK.SRKGKLK.E.T..SE..SSNETQ.K.LTQYFGV..
Retrocopy RTSLHMRDKSQ*LHKNHSELQTSTSRFRRK<KRKCSRKGKLKQEATPRSEH<SSNETQRKALTQYFGVG-

Parental  RFDPPVKKKKIDKSGLEKSIDQAVEEWNIE
          ....P.KK...DKSGLEKSI.QAV.EW.IE
Retrocopy --SIPCKKGINDKSGLEKSIAQAVQEWDIE

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_1079 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 24 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010199	12 retrocopies	retro_chof_1296, retro_chof_1713, retro_chof_1977, retro_chof_2137, retro_chof_2367, retro_chof_2436, retro_chof_2558, retro_chof_2685, retro_chof_590, retro_chof_639, retro_chof_698, retro_chof_832,
Callithrix jacchus	ENSCJAG00000019565	1 retrocopy	retro_cjac_3814,
Cavia porcellus	ENSCPOG00000002747	1 retrocopy	retro_cpor_1356,
Dasypus novemcinctus	ENSDNOG00000001383	2 retrocopies	retro_dnov_138, retro_dnov_167,
Dipodomys ordii	ENSDORG00000002074	1 retrocopy	retro_dord_413,
Echinops telfairi	ENSETEG00000003855	2 retrocopies	retro_etel_1021, retro_etel_944,
Homo sapiens	ENSG00000165669	1 retrocopy	retro_hsap_491,
Gorilla gorilla	ENSGGOG00000010566	1 retrocopy	retro_ggor_460,
Loxodonta africana	ENSLAFG00000016774	4 retrocopies	retro_lafr_1079 , retro_lafr_332, retro_lafr_369, retro_lafr_923,
Macropus eugenii	ENSMEUG00000002674	1 retrocopy	retro_meug_606,
Myotis lucifugus	ENSMLUG00000027454	1 retrocopy	retro_mluc_29,
Macaca mulatta	ENSMMUG00000012741	1 retrocopy	retro_mmul_722,
Monodelphis domestica	ENSMODG00000009378	3 retrocopies	retro_mdom_112, retro_mdom_1258, retro_mdom_38,
Mustela putorius furo	ENSMPUG00000003239	1 retrocopy	retro_mputfur_1400,
Oryctolagus cuniculus	ENSOCUG00000005150	1 retrocopy	retro_ocun_1487,
Otolemur garnettii	ENSOGAG00000028541	1 retrocopy	retro_ogar_1610,
Procavia capensis	ENSPCAG00000011501	1 retrocopy	retro_pcap_400,
Pongo abelii	ENSPPYG00000002694	1 retrocopy	retro_pabe_242,
Pan troglodytes	ENSPTRG00000002984	1 retrocopy	retro_ptro_370,
Pteropus vampyrus	ENSPVAG00000004621	2 retrocopies	retro_pvam_366, retro_pvam_776,
Sorex araneus	ENSSARG00000000819	3 retrocopies	retro_sara_258, retro_sara_323, retro_sara_541,
Sarcophilus harrisii	ENSSHAG00000011601	3 retrocopies	retro_shar_155, retro_shar_412, retro_shar_476,
Tarsius syrichta	ENSTSYG00000009147	1 retrocopy	retro_tsyr_518,
Tursiops truncatus	ENSTTRG00000003351	1 retrocopy	retro_ttru_1322,