RetrogeneDB ID: retro_lafr_1164

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:65132101..65132547(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAM
• Ensembl ID: ENSLAFG00000012891
• Aliases: None
• Description: None

Sequence

>retro_lafr_1164
AAAAAAAAAAAAAAAGAAGATGCTCACAGGGCTGACTGGCAGGCGTTCAAAGAAGAGATAAACAGAATTCGAGAACAGCT
AACTCCAAGTCAGATTGTATCTATGAAAAAGGAAATCATGCAAAAATGTTTAAAAAAGAAAGTATTAATAAGACAAGAAA
GTTAACAATGCTTGGAAGAGAGAAAAGACCTTGCTCAGCTTGTAACATTTTTATATCTGAAAGTTTCCAAGAAACCAAAG
ATGCTTCATCACAGGCAAAGATGAAGACTATAAATGAAAACTGGCAAAATCTGTCTAGTTCTCAAAAGCCAGTATATGTT
CAACTTGCTAAAGATGGTAAAATTCATTATGATAATGAAATGAAATTGTGGGAAGCACAAAAGATTGAAGTTGGGAGAAA
TGGCGTTCTATGTTGCAAAATGAAGCACCGAATAAAAGATGGCTCC

Alignment

ORF - retro_lafr_1164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.67 %
• Parental protein coverage: 60.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKKVYEDAYRADWQAYKEEVNRIQEQLTPSQIVSMEKEIMQKRLKRKALI-KKRELTMLGKPKRPRTAYN
          .KK..EDA.RADWQA.KEE.NRI.EQLTPSQIVSM.KEIMQK.LK.K.LI.K.R.LTMLG..KRP..A.N
Retrocopy KKKKKEDAHRADWQAFKEEINRIREQLTPSQIVSMKKEIMQKCLKKKVLI<KTRKLTMLGREKRPCSACN

Parental  IFISESFQEAKDASSQAKMKTVNENWKNLSSSQKQVYIQLAKDDKIRYDNEMKLWEAQMIEVGRNDLIRR
          IFISESFQE.KDASSQAKMKT.NENW.NLSSSQK.VY.QLAKD.KI.YDNEMKLWEAQ.IEVGRN.....
Retrocopy IFISESFQETKDASSQAKMKTINENWQNLSSSQKPVYVQLAKDGKIHYDNEMKLWEAQKIEVGRNGVLCC

Parental  KMKQRTKDGT
          KMK.R.KDG.
Retrocopy KMKHRIKDGS

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_1164 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 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000535	1 retrocopy	retro_dnov_536,
Dipodomys ordii	ENSDORG00000014013	2 retrocopies	retro_dord_415, retro_dord_691,
Erinaceus europaeus	ENSEEUG00000006119	3 retrocopies	retro_eeur_103, retro_eeur_182, retro_eeur_652,
Homo sapiens	ENSG00000108064	2 retrocopies	retro_hsap_3692, retro_hsap_923,
Gorilla gorilla	ENSGGOG00000004948	2 retrocopies	retro_ggor_2496, retro_ggor_745,
Loxodonta africana	ENSLAFG00000012891	1 retrocopy	retro_lafr_1164 ,
Macropus eugenii	ENSMEUG00000008802	1 retrocopy	retro_meug_190,
Macaca mulatta	ENSMMUG00000019829	1 retrocopy	retro_mmul_1121,
Nomascus leucogenys	ENSNLEG00000012295	2 retrocopies	retro_nleu_2827, retro_nleu_288,
Oryctolagus cuniculus	ENSOCUG00000014405	1 retrocopy	retro_ocun_1278,
Pongo abelii	ENSPPYG00000002430	2 retrocopies	retro_pabe_3042, retro_pabe_796,
Pan troglodytes	ENSPTRG00000002519	1 retrocopy	retro_ptro_641,
Rattus norvegicus	ENSRNOG00000000613	1 retrocopy	retro_rnor_1936,
Tursiops truncatus	ENSTTRG00000009246	1 retrocopy	retro_ttru_1763,