RetrogeneDB ID: retro_lafr_405

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:25563197..25563672(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPAB
• Ensembl ID: ENSLAFG00000001189
• Aliases: None
• Description: None

Sequence

>retro_lafr_405
TGTACAGTAAAAATGAATCCCAAAACTGGACAGTCAAGAGAGCTTGGGCTTCTCTTCAAAGATGCAGCAGCCAGTGTGGC
CCTAGACCAGAAGGAATAGAGGCTGGATGGCCGCATCATCCACCCCAAAAAGGCTAGGTCCCTGAAGAAGGACCCAGTGA
AGAAAATCTTTGTTGGGAGGTCTGAATCCTGAAACCACAGAGGAGATCAGTGAGTACTTTGGCGAGGGTGGGGAGATCTA
GGCCTGCGAGCTTCTCATGGATCCAAAGTTGAACAAAAGAGGAGGCTTTGTTTTCATCACCTAGAAAGAAGAGGAACAAG
TGAAGAAGGTTCTAGAGAAAAAGTTCCACACCATCAGTGGAAGCAAGTGTGAAATCAAAGCGGCTCTGCCCAAAGAGCAG
CCCAGTAGCAGCAGTACTGGTGAAAATGATTGAAATGGAGGTCAGGATAGTACAAATTATGGCTAGAGCCAGAGC

Alignment

ORF - retro_lafr_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.87 %
• Parental protein coverage: 50.46 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CTIKMDPNTGRSRGFGFILFKDATSVEKVLDQKEHRLDGRVIDPKKAMAMKKDPVKKIFVG-GLNPEATE
          CT.KM.P.TG.SR..G..LFKDA......LDQKE.RLDGR.I.PKKA...KKDPVKKIFVG.GLNPE.TE
Retrocopy CTVKMNPKTGQSRELG-LLFKDAAA-SVALDQKE*RLDGRIIHPKKARSLKKDPVKKIFVG>GLNPETTE

Parental  EKIREYFGEFGEIEAIELPMDPKSNKRRGFVFITYKEEEPVKKVLEKKFHTVSGSKCEIKVAQPKEVYQQ
          E.I.EYFGE.GEI.A.EL.MDPK.NKR.GFVFIT.KEEE.VKKVLEKKFHT.SGSKCEIK.A.PKE...Q
Retrocopy E-ISEYFGEGGEI*ACELLMDPKLNKRGGFVFIT*KEEEQVKKVLEKKFHTISGSKCEIKAALPKE---Q

Parental  QQYGSGGRGNRNRGNRGSGGGGQSQS
          ....S.G....N.G...S...G.SQS
Retrocopy PSSSSTGEND*N-GGQDSTNYG*SQS

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_405 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 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000241	2 retrocopies	retro_cfam_408, retro_cfam_412,
Homo sapiens	ENSG00000197451	1 retrocopy	retro_hsap_962,
Loxodonta africana	ENSLAFG00000001189	1 retrocopy	retro_lafr_405 ,
Loxodonta africana	ENSLAFG00000008612	1 retrocopy	retro_lafr_650,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Loxodonta africana	ENSLAFG00000029587	5 retrocopies	retro_lafr_1202, retro_lafr_1208, retro_lafr_192, retro_lafr_747, retro_lafr_961,
Macropus eugenii	ENSMEUG00000007909	2 retrocopies	retro_meug_169, retro_meug_246,
Myotis lucifugus	ENSMLUG00000003380	2 retrocopies	retro_mluc_2024, retro_mluc_2138,
Nomascus leucogenys	ENSNLEG00000015775	1 retrocopy	retro_nleu_1611,
Oryctolagus cuniculus	ENSOCUG00000026424	3 retrocopies	retro_ocun_1800, retro_ocun_1811, retro_ocun_950,
Otolemur garnettii	ENSOGAG00000030251	2 retrocopies	retro_ogar_3509, retro_ogar_385,
Pongo abelii	ENSPPYG00000016107	1 retrocopy	retro_pabe_821,
Pan troglodytes	ENSPTRG00000017601	1 retrocopy	retro_ptro_666,