RetrogeneDB ID: retro_lafr_277

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_11:54162353..54163038(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADIPOR1
• Ensembl ID: ENSLAFG00000003520
• Aliases: None
• Description: None

Sequence

>retro_lafr_277
ATGTCATCTCACAAAGGGTCTGCAGTAGCACAAGGTAATAGGCATCTGTCGGTAATAGGGAAGCTGACACAGTGGAACTG
GCTGAACTGGGACCCCTGCTAGAGGGGCGAATGAGTAATCACCAACCCAATCAAAGATGAAGAGGAGCAAACACTTGCAA
TGCCCCAGGAAGAAGAGGAGGAGGTACAGGTACAGATGCTTTCCCTGCAAACCCACCACAGCATGAAGATAGAGGAGTTT
ATATATAAAGTCTGGGAAGGATGTTGGAGGGTCATCCCATATGATATGCTCTTCAACTGGTGGAAGGAAAATGATGACCT
GCTACATGGCCACAGACCATCCATGCTCTCTTTTTAGGCTTGCTTCAAGAGCCTCTACAGTATCCATACAAAGACTGGCA
AATCTGGATCCACCTGCTCGGTTTCAAGCTATTTCTCTTTTTGGGAATCTTGACCATGCTCAGACCAAATATGTATTTCA
TGGCCTCTCAACAGAAGGAGGTGGTCTTTAGGATGTTCTCTCTGGGTGCGGTGCTCTGCCTCACCTTCTCCTTGTTCTTT
CAAATGTCTACTGTCATTCAGAGAAAGCCTTTTGTACTTTTTCTAAGCTGGACTATTCAGAGACTGCCCTACTGATTATG
GGGGGCTTTGTGCCCTGGCTCTATTACTCATTCTACTGCTCCCCA

Alignment

ORF - retro_lafr_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.95 %
• Parental protein coverage: 61.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSSHKGPVVAQGNG-APASNRETDAVELAELGPLLEEKGKRAVANAA-KTEEEQTCPVPQEEEEEVRVLT
          MSSHKG..VAQGN..A...NRE.D.VELAELGPLLE........N.....E.....P...EEE..V..L.
Retrocopy MSSHKGSAVAQGNR<ASVGNREADTVELAELGPLLEGRMSNHQPNQR>EEEQTLAMPQEEEEEVQVQMLS

Parental  LPLQAHHAMEKMEEFVYKVWEGRWRVIPYDVLPDWLKDNDYLLHGHRPPMPSFRACFKSIFRIHTETG-N
          ..LQ.HH.M.K.EEF.YKVWEG.WRVIPYD.L..W.K.ND.LLHGHRP.M.SF.ACFKS...IHT.TG..
Retrocopy --LQTHHSM-KIEEFIYKVWEGCWRVIPYDMLFNWWKENDDLLHGHRPSMLSF*ACFKSLYSIHTKTG<Q

Parental  IWTHLLGFVLFLFLGILTMLRPNMYFMAPLQEKVVFGMFFLGAVLCLSFSWLFH-TVYCHSEKVSRTFSK
          IW.HLLGF.LFLFLGILTMLRPNMYFMA..Q..VVF.MF.LGAVLCL.FS..F...VYCHSEK...TFSK
Retrocopy IWIHLLGFKLFLFLGILTMLRPNMYFMASQQKEVVFRMFSLGAVLCLTFSLFFQ<NVYCHSEKAFCTFSK

Parental  LDYSGIALLIMGSFVPWLYYSFYCSP
          LDYS..ALLIMG.FVPWLYYSFYCSP
Retrocopy LDYSETALLIMGGFVPWLYYSFYCSP

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_277 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 21 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012199	1 retrocopy	retro_amel_1853,
Choloepus hoffmanni	ENSCHOG00000006450	8 retrocopies	retro_chof_1127, retro_chof_1222, retro_chof_1917, retro_chof_2218, retro_chof_2380, retro_chof_471, retro_chof_749, retro_chof_995,
Callithrix jacchus	ENSCJAG00000006268	3 retrocopies	retro_cjac_2262, retro_cjac_740, retro_cjac_741,
Cavia porcellus	ENSCPOG00000000482	1 retrocopy	retro_cpor_470,
Dipodomys ordii	ENSDORG00000006876	1 retrocopy	retro_dord_19,
Felis catus	ENSFCAG00000013565	1 retrocopy	retro_fcat_1514,
Loxodonta africana	ENSLAFG00000003520	1 retrocopy	retro_lafr_277 ,
Loxodonta africana	ENSLAFG00000021355	1 retrocopy	retro_lafr_249,
Macropus eugenii	ENSMEUG00000015439	1 retrocopy	retro_meug_516,
Microcebus murinus	ENSMICG00000007942	3 retrocopies	retro_mmur_1199, retro_mmur_184, retro_mmur_764,
Myotis lucifugus	ENSMLUG00000016102	2 retrocopies	retro_mluc_1275, retro_mluc_200,
Macaca mulatta	ENSMMUG00000007046	1 retrocopy	retro_mmul_1322,
Mustela putorius furo	ENSMPUG00000011215	1 retrocopy	retro_mputfur_550,
Otolemur garnettii	ENSOGAG00000033821	4 retrocopies	retro_ogar_1558, retro_ogar_1624, retro_ogar_2838, retro_ogar_783,
Ochotona princeps	ENSOPRG00000004528	3 retrocopies	retro_opri_101, retro_opri_1050, retro_opri_392,
Pongo abelii	ENSPPYG00000000342	1 retrocopy	retro_pabe_1072,
Sorex araneus	ENSSARG00000007680	1 retrocopy	retro_sara_25,
Ictidomys tridecemlineatus	ENSSTOG00000015459	3 retrocopies	retro_itri_215, retro_itri_257, retro_itri_512,
Tupaia belangeri	ENSTBEG00000015149	2 retrocopies	retro_tbel_1501, retro_tbel_1804,
Tarsius syrichta	ENSTSYG00000001491	1 retrocopy	retro_tsyr_125,
Tursiops truncatus	ENSTTRG00000006381	2 retrocopies	retro_ttru_1055, retro_ttru_863,