RetrogeneDB ID: retro_lafr_482

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_19:9532672..9532963(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSLAFG00000016460
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_lafr_482
TCCACTTTTAATGATCTGCAAGATCTGAGAGAACAAATTCTTTGAGTTGAAGACACTGATGGTGTTCCAATGATTCTGGT
TGGAAATAAGTGGGACTTAGAAGATGAAAGAGCTGTAGGAAAGGAACAAGGTCAAAATCTAGCATGATAGTGGAACTACT
GTGCATTCTTAGAATCTTCTGCAAAGTCAAAAACAAATGTTAATGAGATCTTTTATGACCTGCTGCGGCAAATTAACAGA
AAAACTCCTGCGCCTGGGAAGGCCCGCAAAAAGTCGTCACATCAGCTGCTT

Alignment

ORF - retro_lafr_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.63 %
• Parental protein coverage: 52.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEI
          STFNDLQDLREQIL.V.DTD.VPMILVGNK.DLEDER.VGKEQGQNLA..WN.CAFLESSAKSK.NVNEI
Retrocopy STFNDLQDLREQIL*VEDTDGVPMILVGNKWDLEDERAVGKEQGQNLA**WNYCAFLESSAKSKTNVNEI

Parental  FYDLVRQINRKTPVPGKARKKSSCQLL
          FYDL.RQINRKTP.PGKARKKSS.QLL
Retrocopy FYDLLRQINRKTPAPGKARKKSSHQLL

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_482 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 31 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Bos taurus	ENSBTAG00000008967	3 retrocopies	retro_btau_1564, retro_btau_297, retro_btau_684,
Callithrix jacchus	ENSCJAG00000007261	3 retrocopies	retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus	ENSDNOG00000019724	18 retrocopies	retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Dipodomys ordii	ENSDORG00000001086	1 retrocopy	retro_dord_521,
Erinaceus europaeus	ENSEEUG00000010052	1 retrocopy	retro_eeur_327,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Homo sapiens	ENSG00000127314	2 retrocopies	retro_hsap_3338, retro_hsap_4234,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482 ,
Loxodonta africana	ENSLAFG00000020706	1 retrocopy	retro_lafr_492,
Microcebus murinus	ENSMICG00000013148	1 retrocopy	retro_mmur_116,
Myotis lucifugus	ENSMLUG00000016606	2 retrocopies	retro_mluc_1126, retro_mluc_2211,
Macaca mulatta	ENSMMUG00000011442	2 retrocopies	retro_mmul_1151, retro_mmul_1863,
Monodelphis domestica	ENSMODG00000007323	5 retrocopies	retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Mus musculus	ENSMUSG00000052681	1 retrocopy	retro_mmus_1370,
Nomascus leucogenys	ENSNLEG00000003573	2 retrocopies	retro_nleu_1034, retro_nleu_481,
Oryctolagus cuniculus	ENSOCUG00000029552	5 retrocopies	retro_ocun_1132, retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Procavia capensis	ENSPCAG00000010977	1 retrocopy	retro_pcap_8,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Pan troglodytes	ENSPTRG00000005197	3 retrocopies	retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sarcophilus harrisii	ENSSHAG00000011497	1 retrocopy	retro_shar_425,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tupaia belangeri	ENSTBEG00000013380	4 retrocopies	retro_tbel_2145, retro_tbel_4650, retro_tbel_4658, retro_tbel_613,
Tarsius syrichta	ENSTSYG00000000192	1 retrocopy	retro_tsyr_910,
Tursiops truncatus	ENSTTRG00000015712	2 retrocopies	retro_ttru_1105, retro_ttru_134,
Vicugna pacos	ENSVPAG00000000931	2 retrocopies	retro_vpac_283, retro_vpac_408,