RetrogeneDB ID: retro_lafr_407

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:33484864..33485785(+)
• Located in intron of: ENSLAFG00000016345

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000021357
• Aliases: None
• Description: None

Sequence

>retro_lafr_407
GAGGCAGTAACGGATGGTCTAGAAATTGTGGTTTCGCCTCGAAGTCTGCACAGTGAGCTGATGTGCCTGATTTGTTTGGG
TTTGCTGAAAAACACTATGACCACAAAGGAGTGTTTGCATCGCTTCTGTGCGGACTGCGTTATCACAGCCTTCAGAAGTG
GCAACAAAGAATGTCCTACCTGTCGGAAAAAGCTAGTTTCCAAAAGATCGCTAAGGCCAGACCCAAACTTTGGTGCCCTC
ATCAGCAAAATTTATCCAAGTCGTGATGAGTCTGAAGCTGACCAGGAGAGAGTATTAGCCAGATCAACAAGCACAACAAT
CAGCAAGCACTCAGTCACAGCATTGAGGAAGGACTGAATATACAGGCCATGAACAGACTACAGCGAGGCAAGAAACAGCA
GATTGAAAATGGTAGTGGAGCAGAAGATAATGGTGACAGTTCCCACTGCAGTAACGCATCCACACATAGCAATCAGGAAG
CAGGACCTAGTAACAAACGGACCAAAACATCTGATGATTCTGGGCTTGAGCTTGATAATAACAATGCAGCAGTGGCAATT
GATCCAGTCATGGATGGTGCTAGTGAAATTGAGTTAGTATTCATGCCTCATCCCACACTTACGGGAAAAAGATGAAAGTG
CACAGACAAGATACATAAAGACTTAAGGTAATGCCACTGTTGATCACTTGTCCAAGTATCTGGCTGTGAGGCTAGCTTTA
GAAGAACTTCGAAGCAAAGGAGAATCAAACCAGATGAACCTTGATACAGCTAGTGAGAAGCAGTATACCATTTACATAGC
AACAGCTAATGGCCAGTTCACTGTATTAAATGGCTCTTTTTCTTTGGAATTGGTCAGTGAGAAATACTGGAAAGTGAACA
AACCCATGGAACTCTATTATGCACCCACAAAAGAGCACAAA

Alignment

ORF - retro_lafr_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRS
          EA.TDGLEIVVSPRSLHSELMC.ICL..LKNTMTTKECLHRFCADC.ITA.RSGNKECPTCRKKLVSKRS
Retrocopy EAVTDGLEIVVSPRSLHSELMCLICLGLLKNTMTTKECLHRFCADCVITAFRSGNKECPTCRKKLVSKRS

Parental  LRPDPNFDALISKIYPSRDEYEAHQERVLAR-INKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGS
          LRPDPNF.ALISKIYPSRDE.EA.QERVLAR.INKHNNQQALSHSIEEGL.IQAMNRLQRGKKQQIENGS
Retrocopy LRPDPNFGALISKIYPSRDESEADQERVLAR<INKHNNQQALSHSIEEGLNIQAMNRLQRGKKQQIENGS

Parental  GAEDNGDSSHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAVAIDPVMDGASEIELVFRPHPT-LM
          GAEDNGDSSHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAVAIDPVMDGASEIELVF.PHPT.L.
Retrocopy GAEDNGDSSHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAVAIDPVMDGASEIELVFMPHPT>LR

Parental  EKDDSAQTSRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATANGQFTVLN
          EKD.SAQT.RYIKT.GNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATANGQFTVLN
Retrocopy EKDESAQT-RYIKT*GNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATANGQFTVLN

Parental  GSFSLELVSEKYWKVNKPMELYYAPTKEHK
          GSFSLELVSEKYWKVNKPMELYYAPTKEHK
Retrocopy GSFSLELVSEKYWKVNKPMELYYAPTKEHK

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_407 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 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011199	3 retrocopies	retro_chof_1450, retro_chof_2217, retro_chof_2251,
Callithrix jacchus	ENSCJAG00000005442	1 retrocopy	retro_cjac_4198,
Erinaceus europaeus	ENSEEUG00000014091	1 retrocopy	retro_eeur_88,
Echinops telfairi	ENSETEG00000015824	1 retrocopy	retro_etel_2081,
Felis catus	ENSFCAG00000009609	1 retrocopy	retro_fcat_1725,
Homo sapiens	ENSG00000121481	2 retrocopies	retro_hsap_4056, retro_hsap_4226,
Gorilla gorilla	ENSGGOG00000014400	1 retrocopy	retro_ggor_2724,
Loxodonta africana	ENSLAFG00000021357	1 retrocopy	retro_lafr_407 ,
Myotis lucifugus	ENSMLUG00000001129	1 retrocopy	retro_mluc_2187,
Monodelphis domestica	ENSMODG00000007422	1 retrocopy	retro_mdom_857,
Nomascus leucogenys	ENSNLEG00000018029	2 retrocopies	retro_nleu_1042, retro_nleu_554,
Oryctolagus cuniculus	ENSOCUG00000004892	1 retrocopy	retro_ocun_838,
Pongo abelii	ENSPPYG00000000417	2 retrocopies	retro_pabe_3331, retro_pabe_3374,
Pan troglodytes	ENSPTRG00000001775	2 retrocopies	retro_ptro_2749, retro_ptro_2871,
Ictidomys tridecemlineatus	ENSSTOG00000006625	3 retrocopies	retro_itri_1646, retro_itri_1794, retro_itri_410,
Tupaia belangeri	ENSTBEG00000016387	4 retrocopies	retro_tbel_1757, retro_tbel_3368, retro_tbel_3892, retro_tbel_4061,
Tarsius syrichta	ENSTSYG00000006109	6 retrocopies	retro_tsyr_1344, retro_tsyr_1647, retro_tsyr_2063, retro_tsyr_2083, retro_tsyr_227, retro_tsyr_474,