RetrogeneDB ID: retro_lafr_1035

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:66665194..66665982(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSLAFG00000008844
• Aliases: None
• Description: None

Sequence

>retro_lafr_1035
AGAATGGGAGAGCTGATGACCAGGCCTACAGGCCTGAGATGTGCATCTGTAAGTGTACGTGCAGCCAAAGAAGAGGAGTC
CAAAGAGCAGCAGGTGAAAGCAGAGCCACTCCCTTTACGTATTGCACCACCTCTCCAGCCTCAATATGTTGAAGAACAGC
CTGGTCATTTACAAATGGGCTTTGCCTCCGTCCGTACTACAGCTGGTCGTTAAATTGGCTGGTGCAAGGATGTATATGTC
TTTGTGAAAAATGGGATAAGGGATACAGTACAATTTGGAAAAGATGCATATGTTTATCTGAAGAACCCGGCATGGCGATT
TTCTTCCCGAAATCGGAGTGATTACAATTTCAGAATTGGCAGGCCTGGTTTCAGTGAGAAAAGGTTCCAGAGTTAAGAAA
ATTGCTTATCCGCTGGGACTAGCCACTTTAGGAGCAACTGTTTGCTGCCCAGTTCAGTCAGTGATAATTGCAAAGGTAGC
TGGGAAAAAAGCATATGCCCCAAGCCAGCAAATTTATGAAGCAGTTTAATCATCGTGGACCAAAAAATAAAAAAAGAATC
ACTCCCTGAACCTAAAGAAAAAACTAAGGTAGAAGTTATGCTGAAATAGAAATACCTACAAAGGCAATTCAAGTCCTGAA
ACATTCAGTGCCTTAGCCAACAGAACTCAGCTCTGAAACAAAGGCCAGATGGGAACGCACCTCAGGTGCTCCGCAGTTTA
TGCCTGACCCCAGGCTCATGGGTCACGGGCAGTCCCACCCAGAAGATGGAGATACATACAGCACTAGA

Alignment

ORF - retro_lafr_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.53 %
• Parental protein coverage: 98.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QMGKLTTLPTGLICASVSVRAAKEEDPRKQLVKPEQLPIYTAPPLQSKYVEEQPGHLQMGFASIRTTTGR
          .MG.L.T.PTGL.CASVSVRAAKEE....Q.VK.E.LP...APPLQ..YVEEQPGHLQMGFAS.RTT.GR
Retrocopy RMGELMTRPTGLRCASVSVRAAKEEESKEQQVKAEPLPLRIAPPLQPQYVEEQPGHLQMGFASVRTTAGR

Parental  YVGWFKGVYVFVKNGIMDTVQFGKDAYVYLKNPP-GDFLPKIGVITVSGLAGLVSARKGSRFKKIAYPLG
          ..GW.K.VYVFVKNGI.DTVQFGKDAYVYLKNP..GDFLP.IGVIT.S.LAGLVS.RKGSR.KKIAYPLG
Retrocopy *IGWCKDVYVFVKNGIRDTVQFGKDAYVYLKNPA>GDFLPEIGVITISELAGLVSVRKGSRVKKIAYPLG

Parental  LATVGATVCYPVQSIIIAKVTGKKAYAVSQQIYEAVKSLWTK-SNKKESLPEPKEKTEV-GSYAETEIPT
          LAT.GATVC.PVQS.IIAKV.GKKAYA.SQQIYEAV.S.WTK...KKESLPEPKEKT.V..SYAE.EIPT
Retrocopy LATLGATVCCPVQSVIIAKVAGKKAYAPSQQIYEAV*SSWTK<KIKKESLPEPKEKTKV<RSYAEIEIPT

Parental  KTTQALKHSVPLPTELSSETKTKSEPTSAGATQFIPDPKLMDHGQSHPEDVDMYSTR
          K..Q.LKHSVP.PTELSSETK...E.TS.GA.QF.PDP.LM.HGQSHPED.D.YSTR
Retrocopy KAIQVLKHSVP*PTELSSETKARWERTS-GAPQFMPDPRLMGHGQSHPEDGDTYSTR

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_1035 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.

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253,
Gorilla gorilla	ENSGGOG00000016329	1 retrocopy	retro_ggor_2213,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035 ,
Loxodonta africana	ENSLAFG00000029070	1 retrocopy	retro_lafr_1114,
Microcebus murinus	ENSMICG00000015844	1 retrocopy	retro_mmur_1511,
Myotis lucifugus	ENSMLUG00000011384	1 retrocopy	retro_mluc_1364,
Macaca mulatta	ENSMMUG00000004335	1 retrocopy	retro_mmul_2045,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys	ENSNLEG00000002634	1 retrocopy	retro_nleu_1702,
Pongo abelii	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tupaia belangeri	ENSTBEG00000010147	5 retrocopies	retro_tbel_2037, retro_tbel_2609, retro_tbel_2840, retro_tbel_3361, retro_tbel_3737,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,