RetrogeneDB ID: retro_lafr_1119

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_70:8323142..8323674(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC3
• Ensembl ID: ENSLAFG00000006166
• Aliases: None
• Description: None

Sequence

>retro_lafr_1119
GCCTACCACTCTTCTCTCGTGGACCCTGACACCAAACTCATTAGAAACATGGTGCTGCTACGTATCGTATCAGAAGTCAG
TTCAAAGGACCCGCCCCTCAAGAGACAAAAGATGCAGATATCATGGACGAGGCCGTCCATTACTTCAAGGCCAACGTCTT
CTGCAGAAACTATGAAATTAAGAATGGAGCAGATAGGACCTCGATATATATAACTCTCTACATTTCTGAATGCCTAAAGA
AACTCTAGAAGTACAATTCCAAAAGCCAAGGCAAGAAAGAAATATACACACTGGGAATCACTAACTCCCCTATTCCTGGA
GAGCCTGGTTTTCCATTTAATGCCATTCATGCCAAACCTGCAAACAAGGAGGAAGATGAAGTGATGAGGGTGTACTTACA
GCAGCTAAGGCAAGAGAGGGACTGAGGCTTTGTGAGAAAGTTTTTGACCCTCTGAATGACAAACCTAGGAAGTGGTGGAC
TTGCTTTGTGAAGAGACAGTTCATGAACAAGAGTCTTTCAGGACCTGGACAG

Alignment

ORF - retro_lafr_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.22 %
• Parental protein coverage: 98.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AYHSSLMDPDTKLIGNMALLPIRSQF--KGP-APRETKDTDIIDEAIYYFKANVFFKNYEIKNEADRTLI
          AYHSSL.DPDTKLI.NM.LL.I.S....K.P.AP.ETKD.DI.DEA..YFKANVF..NYEIKN.ADRT.I
Retrocopy AYHSSLVDPDTKLIRNMVLLRIVSEVSSKDP<APQETKDADIMDEAVHYFKANVFCRNYEIKNGADRTSI

Parental  YITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQE
          YITLYISECLKKL.K.NSKSQG.KE.YTLGITN.PIPGEPGFP.NAI.AKPANK.EDEVMR.YLQQLRQE
Retrocopy YITLYISECLKKL*KYNSKSQGKKEIYTLGITNSPIPGEPGFPFNAIHAKPANKEEDEVMRVYLQQLRQE

Parental  -TGLRLCEKVFDPLNDKPSKWWTCFVKRQFMNKSLSGPGQ
          ..GLRLCEKVFDPLNDKP.KWWTCFVKRQFMNKSLSGPGQ
Retrocopy <EGLRLCEKVFDPLNDKPRKWWTCFVKRQFMNKSLSGPGQ

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_1119 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 18 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Dasypus novemcinctus	ENSDNOG00000004987	2 retrocopies	retro_dnov_2619, retro_dnov_685,
Erinaceus europaeus	ENSEEUG00000011531	2 retrocopies	retro_eeur_122, retro_eeur_99,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Loxodonta africana	ENSLAFG00000006166	3 retrocopies	retro_lafr_1119 , retro_lafr_763, retro_lafr_840,
Macaca mulatta	ENSMMUG00000006492	3 retrocopies	retro_mmul_1105, retro_mmul_1174, retro_mmul_543,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Nomascus leucogenys	ENSNLEG00000002802	4 retrocopies	retro_nleu_239, retro_nleu_283, retro_nleu_3078, retro_nleu_389,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Otolemur garnettii	ENSOGAG00000013424	1 retrocopy	retro_ogar_2855,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Procavia capensis	ENSPCAG00000011858	2 retrocopies	retro_pcap_421, retro_pcap_441,
Pongo abelii	ENSPPYG00000004947	6 retrocopies	retro_pabe_1735, retro_pabe_1790, retro_pabe_2838, retro_pabe_376, retro_pabe_769, retro_pabe_792,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Tarsius syrichta	ENSTSYG00000002953	4 retrocopies	retro_tsyr_1150, retro_tsyr_1341, retro_tsyr_2103, retro_tsyr_794,
Tursiops truncatus	ENSTTRG00000015083	2 retrocopies	retro_ttru_713, retro_ttru_880,
Vicugna pacos	ENSVPAG00000008404	1 retrocopy	retro_vpac_225,