RetrogeneDB ID: retro_lafr_1073

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_66:2263426..2264060(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000030301
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3I
• Ensembl ID: ENSLAFG00000017026
• Aliases: None
• Description: None

Sequence

>retro_lafr_1073
GTGTGGTGTGTGGATCCCAACTGGAACACCAAGCATGTCCTCACTGGCTCAGTTGACAACATCTGTCGTTTCTGGGACTG
TGAAACAGGGAAGCAGCTGGCCCTACTCAAGACCTACTCAGCTGTCCGAACCTGTGGCCTTGACTGTGGGGGCAATATCA
TCATGTTCTGTACGGACAACCGTATGGGATACCAGTGCTTTGTGAACTTCTTCAGCCTGAAGGACCCAAGCCAGATCACC
AACAATAGTGAGCGCTACATGATGATCCCTTGCAATGACCCCAAGATCACCAGTGCAGTGTGGGGGCCCCTGAGAGAGTG
TGTCTTCACAAGACCATGAGAGTGGAGAGCTCAACCAGTACAGCACCAAGTCTGGAGAGGTATTGGTGAATGTTAAGGAG
CACTCCTGGCAGATCAGTGACATACAATTATCCAGGGATATGACCATGTTTATCACCACATCCAAGGACAACACAGCTAA
GCTCTTTGACTCCACAACCCTTGAATACCAGCAGACTTTCCAGACAGAACGTCCTGTCAACTCAGCTGCCCTATTTCCCA
ACTATGACCATGTGGCTCTAGGTAGTGGTCAAGAAGCCATGGATCTAACCACGACCTCCACCAGGACTAACAAA

Alignment

ORF - retro_lafr_1073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.66 %
• Parental protein coverage: 64.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VWCVDADWDTKHVLTGSADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFVSF
          VWCVD..W.TKHVLTGS.DN.CR.WDCETGKQLALLKT.SAVRTCG.D.GGNIIMF.TD..MGYQCFV.F
Retrocopy VWCVDPNWNTKHVLTGSVDNICRFWDCETGKQLALLKTYSAVRTCGLDCGGNIIMFCTDNRMGYQCFVNF

Parental  FDLRDPSQIDSN-EPYMKIPCNDSKITSAVWGPLGECIIA-GHESGELNQYSAKSGEVLVNVKEHSRQIN
          F.L.DPSQI..N.E.YM.IPCND.KITSAVWGPL.EC.....HESGELNQYS.KSGEVLVNVKEHS.QI.
Retrocopy FSLKDPSQITNNSERYMMIPCNDPKITSAVWGPLRECVFT>DHESGELNQYSTKSGEVLVNVKEHSWQIS

Parental  DIQLSRDMTMFVTASKDNTAKLFDSTTLEHQKTFRTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRI
          DIQLSRDMTMF.T.SKDNTAKLFDSTTLE.Q.TF.TERPVNSAAL.PNYDHV.LG.GQEAMD.TTTSTR.
Retrocopy DIQLSRDMTMFITTSKDNTAKLFDSTTLEYQQTFQTERPVNSAALFPNYDHVALGSGQEAMDLTTTSTRT

Parental  GK
          .K
Retrocopy NK

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_1073 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010674	1 retrocopy	retro_cfam_321,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Homo sapiens	ENSG00000084623	2 retrocopies	retro_hsap_3888, retro_hsap_3894,
Gorilla gorilla	ENSGGOG00000001579	3 retrocopies	retro_ggor_2540, retro_ggor_2615, retro_ggor_2623,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073 ,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Mus musculus	ENSMUSG00000028798	2 retrocopies	retro_mmus_1375, retro_mmus_607,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129, retro_nleu_1135,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169, retro_pabe_3175,
Rattus norvegicus	ENSRNOG00000047185	1 retrocopy	retro_rnor_1548,