RetrogeneDB ID: retro_lafr_820

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:83902653..83903978(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000013424
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDIA6
• Ensembl ID: ENSLAFG00000012281
• Aliases: None
• Description: None

Sequence

>retro_lafr_820
GCGCTCAGCATAGCTCACCTAGTGCTTGGTCTGGTGAGCTATACCTTCTTCCTAGCAGTGAGTGGTCTATATTCTTCCAA
TGATGATGTAATTGAATTAATGCCATCAAATTTCAACCAAGAAGTTATTCAAAGTGATAGTTTGTGGCTTGTAGAATTCT
ATGCTCCATGGTGTGGCCACTGCCAAAGATTAACACCAGAATGGAAGAAAAGTAAGAACTGCATTAAAAGATATTGTAAA
AGTTGGTGCAGTTGATGCAGATAAGCATCAGTCCCTAGCAGGGCAGTATGGCCTTCAGGGATTTCCTACCATCAAGATTT
TTAGATCCATCAAAAACAAACCTGAAGATTATCAGGGTGGCAGAACAGCTGAAGCCGTTGTAGATGCATCTCTCAGTGCT
GTAGGACAGCTGGTAAAGGATCGTCTTGGGGGAAAGAGTGGTGGATACAGTTCTGGAAAACAAGGCAGAAGTGAAAGTTC
AAGTAAGAAAGACGTGATTGAACTGATAAATGACACCTTTGATAAAAACGTTCTTGATGTTTGGATAGTCGAGCTTTATG
CTCCTTGGCGTGGACACTGCAAAAATCTAGAGCCAGAATGGGCTGCTGCACCTACAGAGGTAAAAGATCAAACAAAAGAA
AAAGTGAAACTAGCAGCTGTAGATGCTACAGTTAATCAGGTGCTAGCCAGCCGATATGGGTTTAAGGGATTTCCTACAAT
CAAGATTTTTTTCAGAAAGGCGAGTCTCCTGTGGTTTACAATGGCAGCCGGACAAAATCTGACATAGTTTTACGGGCCTT
AGATTTGTTTTCTGATAATGCCCCACCTCCTGAGCTGCTTGAGATAATTAATGAGGACATTGCCAAGAAGACTTGTGAAG
ATCATCAGCTCTGTGTTGTGGCTGTGCTGCCCCACATTCTCGATACTGGAGCTGCAGGCAGAAATTCATATTTGGAAGTT
TTTCTGAAGTTGGCAGAAAAATACAAAAAGAAAATGTGGGGGTGTCTGTGGGCAGAAGTTGGAGCCCCGTATGAACTTGA
GAACGTGTTGGGGTTTGGAGGGTTTGGATACCCGGCCATGGCAGCCATCAATGACGCAAGATGAAATTTGCTCTTCTGAA
AGGGTCTTTCAGTGAACGAGGCATTAATGAGTTTCTCAGGGAGCTCTCTTTTGGGCGTGGATCCACAGCACCTGTAGGGG
GTGGGGCCTTCCCTAATATAAGTACAATAATAGAACCTTGGGATCGCAAGGATGGTGAACTTCCTGTGGAGGATGATACC
GATCTCAGTGATGGGAAGCTTGATGACTTAGGGAAAGATGAGTTG

Alignment

ORF - retro_lafr_820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ALSMARLVLGLVSCTFFLAVNGLYSSSDDVIELTPSNFNREVIQSDSLWLIEFYAPWCGHCQRLTPEWKK
          ALS.A.LVLGLVS.TFFLAV.GLYSS.DDVIEL.PSNFN.EVIQSDSLWL.EFYAPWCGHCQRLTPEWKK
Retrocopy ALSIAHLVLGLVSYTFFLAVSGLYSSNDDVIELMPSNFNQEVIQSDSLWLVEFYAPWCGHCQRLTPEWKK

Parental  -VATALKDVVKVGAVDADKHQSLAGQYGVQGFPTIRIFGSNKNRPEDYQGGRTAEAIVDAALSAVRQLVK
          .V.TALKD.VKVGAVDADKHQSLAGQYG.QGFPTI.IF.S.KN.PEDYQGGRTAEA.VDA.LSAV.QLVK
Retrocopy >VRTALKDIVKVGAVDADKHQSLAGQYGLQGFPTIKIFRSIKNKPEDYQGGRTAEAVVDASLSAVGQLVK

Parental  DRLGGRSGGYSSGKQGRSESSSKKDVIELTDDTFDKNVLESEDVWMVEFYAPWCGHCKNLEPEWAAAATE
          DRLGG.SGGYSSGKQGRSESSSKKDVIEL..DTFDKNVL...DVW.VE.YAPW.GHCKNLEPEWAAA.TE
Retrocopy DRLGGKSGGYSSGKQGRSESSSKKDVIELINDTFDKNVL---DVWIVELYAPWRGHCKNLEPEWAAAPTE

Parental  VKDQTKGKVKLAAVDATVNQVLASRY-GIRGFPTIKIF-QKGESPVDYDGGRTKSDIVSRALDLFSDNAP
          VKDQTK.KVKLAAVDATVNQVLASRY.G.R.F.....F.QKGESPV.Y.G.RTKSDIV.RALDLFSDNAP
Retrocopy VKDQTKEKVKLAAVDATVNQVLASRY>GLRDFLQSRFF>QKGESPVVYNGSRTKSDIVLRALDLFSDNAP

Parental  PPELLEIINEDIAKKTCEDHQLCVVAVLPHILDTGAAGRNSYLEVLLKLADKYKKKMWGWLWAEAGAQYE
          PPELLEIINEDIAKKTCEDHQLCVVAVLPHILDTGAAGRNSYLEV.LKLA.KYKKKMWG.LWAE.GA.YE
Retrocopy PPELLEIINEDIAKKTCEDHQLCVVAVLPHILDTGAAGRNSYLEVFLKLAEKYKKKMWGCLWAEVGAPYE

Parental  LENALGIGGFGYPAMAAINA-RKMKFALLKGSFSEQGINEFLRELSFGRGSTAPVGGGAFPKIST-VEPW
          LEN.LG.GGFGYPAMAAIN..RKMKFALLKGSFSE.GINEFLRELSFGRGSTAPVGGGAFP.IST..EPW
Retrocopy LENVLGFGGFGYPAMAAIND<RKMKFALLKGSFSERGINEFLRELSFGRGSTAPVGGGAFPNISTIIEPW

Parental  DGKDGELPVEDDIDLSDVELDDLGKDEL
          D.KDGELPVEDD.DLSD..LDDLGKDEL
Retrocopy DRKDGELPVEDDTDLSDGKLDDLGKDEL

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_820 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001928	1 retrocopy	retro_btau_358,
Loxodonta africana	ENSLAFG00000012281	1 retrocopy	retro_lafr_820 ,
Tarsius syrichta	ENSTSYG00000013891	1 retrocopy	retro_tsyr_1661,