RetrogeneDB ID: retro_lafr_1051

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_61:5382814..5383375(-)
• Located in intron of: ENSLAFG00000005760

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE4A
• Ensembl ID: ENSLAFG00000004214
• Aliases: None
• Description: None

Sequence

>retro_lafr_1051
CTGATAGCCTATGACTCCTGAAAAAATATCACACAAAACAGCAGAAAACATCTTTAATAAAACCCATACATTCCACTTTC
TGTTGGGTTCAGTACACGGAGAGCTCCCTGTGCCAAAGCTAGGAGCTGATCATCCAAGAAACGTTTGTATGATAGAAGAG
CAGAGGGCAATTCCTGCCTGTTTAAAAACAATGGAAGAATCTTACCAAGAAATAACAGAAAAAGAGGTAGAAAGAATCTT
GGGATTGTTTCAAACATATTTTCAAGAAGATACTGATACACCTATGTCCTTCTTTGACTTTGTGGTTGATCTACATTCTT
TTTCCCATGAGAGAGAAATCATCTTTCATGTTTCCTTCATTATAAGGGATGGTTTTGTAAGAATAAGACTTGATGAAGAT
TGACTACAAATAATGAAGCCTATTAATATCAACCAGGAAAATGAGGGAGTTGACCCTAACACCCAAATTAGGCATCAAGG
ATTTATAGTTTTGAGTTACTGGGACTGGGAAGAGATTGGAAGACCTTCAAGATTTCAGTGCCTGTGATTGCTTCAGGTCA
G

Alignment

ORF - retro_lafr_1051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.84 %
• Parental protein coverage: 55.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLVYDSWKR-AGKTAENTFNKTHTFHFLLGSIQGEPPEPKPRADRPKKTRTTEEQRVMPTQLKRMEESHQ
          L..YDS.K....KTAEN.FNKTHTFHFLLGS..GE.P.PK..AD.P......EEQR..P..LK.MEES.Q
Retrocopy LIAYDS*KN>SHKTAENIFNKTHTFHFLLGSVHGELPVPKLGADHPRNVCMIEEQRAIPACLKTMEESYQ

Parental  EATEKEVERILGLLQTYFQEDPDTPISFFDFVVDPHSFPRTVENIFHVSFIIRDGFARIRLDDDRLPVIE
          E.TEKEVERILGL.QTYFQED.DTP.SFFDFVVD.HSF....E.IFHVSFIIRDGF.RIRLD.D.L....
Retrocopy EITEKEVERILGLFQTYFQEDTDTPMSFFDFVVDLHSFSHEREIIFHVSFIIRDGFVRIRLDED*LQIMK

Parental  PVNTNEENEGVDHNTQTRHQGIIALSYRDWEEI-VKTFEISEPVIASSQ
          P.N.N.ENEGVD.NTQ.RHQG.I.LSY.DWEEI..KTF.IS.PVIAS.Q
Retrocopy PININQENEGVDPNTQIRHQGFIVLSYWDWEEI<WKTFKISVPVIASGQ

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_1051 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051 ,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,