RetrogeneDB ID: retro_lafr_1210

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:12082022..12083202(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSLAFG00000001107
• Aliases: None
• Description: eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]

Sequence

>retro_lafr_1210
GGTCCTGATGGGATGGAGCCCAAAGGTGTCATCAAGAGTAACTAGAATGAGACTATTGATAGCTTTGATGACATGAACCT
CTCAGAGTTCCTGCTCTGAGGCATCTACACGTATGGTTTCAAGAAGCCTTCTGCCATCCAGCAACGAGCCTTCTCCCTTG
TATCGAGGGTTATGATGTGATCTCTCGAGCCCAATCTGGGACCATAAAAATGGCCTCTTTTCCCACATCAATCCTACAGC
AGATTGAATAAGATCTAAGGGTCACCCGAGCCTTGGTTCTGGCTCCCGCTAGAGAACTGATCCAGCAGATACAGAAAGTG
GTGCTGACATTAGGAGATTACATGGGTGCCTCCTACCATGCCTGCATTGGGGGCATTAACATGTGTGCTGAAGTGCAGAA
GCTGCAAATGGAGGCTCCCCCTATCATCGTGGGTACCCCAGGCTGTGTGTTTGATATGCTTAATTGAAGATACTTGCCTC
CCAAATACATCAGGATGTTTATACTGGATGAAGCTGGTCAAATGCTAAGCCATGGATTCAAGGACCATATCTATGGCATA
TTCCAAAAGCTCGATTGCAACACTCAGGTAGTTTTGCTGTCAGGTACAATGCCTCCTGATATGCTTGAGGTGACCAAGAA
ATTCATGAGGGACCCCATTCAGATCCTTGTCAAGAAGAAACAATTCACCCTGGAGGGTACTGGCCAATTCTACGACAATG
TGAAACAAGAGGAGTGGAAATCGGATACACTGTGTGATTTGTGTGAAACCTTGACCATTATCCAGGCAGTCATCTTCATT
AACACCCAGAGGAAGGTTGTTTGGCTCTCTGAGAAGATGCATGCCTGAGACTTTACTGTTTCTGTCACGCATGGAGATTT
AAACCAAAAGGAATGAGACGTGATCATGAAACAGTTCCATTCTGGTTCTAGCAGAGTACTGATTCCACTGACCTACTGGC
CAGAGGCATTGATGTGCAGCAGGTTTCTTTAGTCATCAACTATGACCTTCCCACCAACAGGAAAAACTGTATCCACAGAA
TCAATCTTGGTAGATATTTTGGCTATAAGGGTGTGTCTATTAACATGGTGACAAAAGAAGACAAGAGGATTCTTCCAGAC
CTCGAGACCATCTACAACACCTCTGTTGAGGAGATACCCCTCAATGTTGCTGACCTCATC

Alignment

ORF - retro_lafr_1210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 97.04 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRA-ILPCIKGYDVIAQAQSGTG
          GPDGMEP.GVI.SN.NE..DSFDDMNLSE.LL.GIY.YGF.KPSAIQQRA..LPCI.GYDVI..AQSGT.
Retrocopy GPDGMEPKGVIKSN*NETIDSFDDMNLSEFLL*GIYTYGFKKPSAIQQRA<LLPCIEGYDVISRAQSGTI

Parental  KTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEA
          K.A.F..SILQQIE.DL..T.ALVLAP.REL.QQIQKVV..LGDYMGAS.HACIGG.N..AEVQKLQMEA
Retrocopy KMASFPTSILQQIE*DLRVTRALVLAPARELIQQIQKVVLTLGDYMGASYHACIGGINMCAEVQKLQMEA

Parental  PHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVL
          P.IIVGTPG.VFDMLN.RYL.PKYI.MF.LDEA..MLS.GFKD.IY.IFQKL..NTQVVLLS.TMP.D.L
Retrocopy PPIIVGTPGCVFDMLN*RYLPPKYIRMFILDEAGQMLSHGFKDHIYGIFQKLDCNTQVVLLSGTMPPDML

Parental  EVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEK
          EVTKKFMRDPI.ILVKK...TLEG..QFY.NV..EEWK.DTLCDL.ETLTI.QAVIFINT.RKV.WL.EK
Retrocopy EVTKKFMRDPIQILVKKKQFTLEGTGQFYDNVKQEEWKSDTLCDLCETLTIIQAVIFINTQRKVVWLSEK

Parental  MHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLI-TTDLLARGIDVQQVSLVINYDLPTNRENYIHRI
          MHA.DFTVS..HGD..QKE.DVIM..F.SGSSRVLI..TDLLARGIDVQQVSLVINYDLPTNR.N.IHRI
Retrocopy MHA*DFTVSVTHGDLNQKE*DVIMKQFHSGSSRVLI<STDLLARGIDVQQVSLVINYDLPTNRKNCIHRI

Parental  GRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
          ..G..FG.KGV.INMVT.EDKR.L.D.ET.YNTS.EE.PLNVADLI
Retrocopy NLGRYFGYKGVSINMVTKEDKRILPDLETIYNTSVEEIPLNVADLI

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_1210 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 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000132	1 retrocopy	retro_btau_1207,
Loxodonta africana	ENSLAFG00000001107	1 retrocopy	retro_lafr_1210 ,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Oryctolagus cuniculus	ENSOCUG00000010375	5 retrocopies	retro_ocun_1020, retro_ocun_1326, retro_ocun_1375, retro_ocun_475, retro_ocun_934,
Pongo abelii	ENSPPYG00000007926	7 retrocopies	retro_pabe_1090, retro_pabe_1474, retro_pabe_3759, retro_pabe_3792, retro_pabe_548, retro_pabe_846, retro_pabe_987,