RetrogeneDB ID: retro_lafr_412

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:50989149..50989539(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OOEP
• Ensembl ID: ENSLAFG00000012754
• Aliases: None
• Description: None

Sequence

>retro_lafr_412
ATGGTGGATAATGCTGGTGGTCCTGAGGCCCAAGTGGAGCGAGATTCCCTTGTGTTACCGCAACAAGGACCAACACTTTG
CTTGCGGCCATGGTGGTTTCCGGTGGAGGAATTAAAGGAACTGCTGGTGTTTTGCCTGGAGGCATGGCTGGTGGACCTGA
TCTTTGGCCCAGATCAAGCCATAATTCCAAAAATTGAGTGGATTAGCCAGGCTCTGCTGACTGTGGACGTAGTGGACTCC
AGGGACGTAGACAAAATCACAATCTTCGGACGGCCTAGGGTACAGGATCGGGTGAAGAAGGTGCTCCTGCCCATGGCATC
TTGGCACTGGAAACGTCACTGAAGTGAGAAGACGGACCAGCTCGAGGAGTTCTTGAAGGAGGGTGCATCA

Alignment

ORF - retro_lafr_412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.44 %
• Parental protein coverage: 99.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVDNAGGAEAQVEPDSLVLPHQGPTLRLRPWWFPVEELKEPLVFYLDSWLVDLIFGPDRAIIPKIEWMSQ
          MVDNAGG.EAQVE.DSLVLP.QGPTL.LRPWWFPVEELKE.LVF.L..WLVDLIFGPD.AIIPKIEW.SQ
Retrocopy MVDNAGGPEAQVERDSLVLPQQGPTLCLRPWWFPVEELKELLVFCLEAWLVDLIFGPDQAIIPKIEWISQ

Parental  ILLTVDVVDSSDLAKITIFGRPRVQNRVKKVLLAVASWHRKRRHRSEKMEQLEEFLKAGAS
          .LLTVDVVDS.D..KITIFGRPRVQ.RVKKVLL..ASWH.K.RH.SEK..QLEEFLK.GAS
Retrocopy ALLTVDVVDSRDVDKITIFGRPRVQDRVKKVLLPMASWHWK-RH*SEKTDQLEEFLKEGAS

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_412 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 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009962	1 retrocopy	retro_cjac_3033,
Homo sapiens	ENSG00000203907	3 retrocopies	retro_hsap_432, retro_hsap_4807, retro_hsap_543,
Gorilla gorilla	ENSGGOG00000016832	3 retrocopies	retro_ggor_2992, retro_ggor_422, retro_ggor_495,
Loxodonta africana	ENSLAFG00000012754	2 retrocopies	retro_lafr_412 , retro_lafr_782,
Myotis lucifugus	ENSMLUG00000017174	2 retrocopies	retro_mluc_115, retro_mluc_252,
Macaca mulatta	ENSMMUG00000000416	2 retrocopies	retro_mmul_2561, retro_mmul_519,
Nomascus leucogenys	ENSNLEG00000001204	2 retrocopies	retro_nleu_2182, retro_nleu_717,
Oryctolagus cuniculus	ENSOCUG00000025904	1 retrocopy	retro_ocun_20,
Pan troglodytes	ENSPTRG00000029545	3 retrocopies	retro_ptro_3197, retro_ptro_329, retro_ptro_408,
Rattus norvegicus	ENSRNOG00000025957	1 retrocopy	retro_rnor_2192,
Tursiops truncatus	ENSTTRG00000001487	2 retrocopies	retro_ttru_1376, retro_ttru_1803,