RetrogeneDB ID: retro_lafr_702

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_31:536761..537070(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FIS1
• Ensembl ID: ENSLAFG00000020494
• Aliases: None
• Description: None

Sequence

>retro_lafr_702
CTAAACGAGTTATGTCCGTGAACAACCTGCTGAAATGTCAAGAGAAGTGTCTGTCTGAGAAGGCAGCAGGTTCAGTGGCC
AAGAACATGCAGCTCAAGTACACCTCGTGCCTGGCATGAAGCAAGTACAGTGATGACATCCTCAAAAGCATCAGGCTGCT
GGAGGAGCTGCAGTCCAAAGGGAGCAAGAGGACCAATAGAACTTCATCTTCTACCTAGTTGAGAGTGCTACCAGCTCAAG
GAACGTGGAACGGTTCTAAGGTCAACATCAGAGCTGCTACAGCACAGCAACCAGGCTAAGGAGCTGAAG

Alignment

ORF - retro_lafr_702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.82 %
• Parental protein coverage: 70.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LNEL-VSVDDLLKFERKFQSEKAAGAVSKSTQFEYAWCLVRSKYNDDIRKGIALLEELLPKGSK-EEQRD
          LNEL..SV..LLK...K..SEKAAG.V.K..Q..Y..CL..SKY.DDI.K.I.LLEEL..KGSK.E.Q..
Retrocopy LNEL<MSVNNLLKCQEKCLSEKAAGSVAKNMQLKYTSCLA*SKYSDDILKSIRLLEELQSKGSK<EDQ*N

Parental  YVFYLAVGN-YRLKEYEKALKYVRGLLQTEPQNTQAKELE
          ..FYL.....Y.LKE....L.....LLQ......QAKEL.
Retrocopy FIFYLVESA<YQLKERGTVLRSTSELLQ---HSNQAKELK

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_702 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013800	2 retrocopies	retro_cfam_557, retro_cfam_755,
Callithrix jacchus	ENSCJAG00000016053	1 retrocopy	retro_cjac_1913,
Loxodonta africana	ENSLAFG00000020494	1 retrocopy	retro_lafr_702 ,
Myotis lucifugus	ENSMLUG00000024207	1 retrocopy	retro_mluc_168,
Monodelphis domestica	ENSMODG00000005034	1 retrocopy	retro_mdom_1773,
Otolemur garnettii	ENSOGAG00000028158	1 retrocopy	retro_ogar_1544,
Rattus norvegicus	ENSRNOG00000001420	2 retrocopies	retro_rnor_1659, retro_rnor_1689,
Sus scrofa	ENSSSCG00000027757	1 retrocopy	retro_sscr_1083,