RetrogeneDB ID: retro_lafr_679

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_3:55417379..55417834(-)
• Located in intron of: ENSLAFG00000018521

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000022560
• Aliases: None
• Description: None

Sequence

>retro_lafr_679
CTCTCCAGGAAGGTGAAAGGGCCTGTCCTGGACAACTTCCGGTCGGTGGAAGGCCAAATCGAAGGCCTCACAGATGAATC
TGAAGAACTAGAGCTCTTAAGTATAATCAATGCAGGCTTCACCTCTGTGGCAAACTTACCGAAGTTAGATAAACATAAGA
AGCTTGAACTAAGCAGTAAAAGAATCTCAGGGGGCCTGGAAGTATTGGCAGAAAAGTGCCTGAACCTCACACATTTAAAT
TTAAGTGGCAACAAAATTAAAGGCCTCAGTACAATAGAGCCACTGAAAAGTCAGAAAACCTCAAGAGCTTAGACCTGTTC
AATCGTAAGCTAACCAACCTGAAGGACTACAGAGAAAACGTGCTCAGGCTCCTCCCACAACTCACGTATCTCGATGGCTT
AAGACCTGACGGCCAGGAGGCCCCTGACTCGGATGCCTAGGGCGACGTGGAGGGC

Alignment

ORF - retro_lafr_679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPLQVKELVLDNCRSIEGKIEGLTDEFEELEFLSTINVGLTSVANLPKLNKLKKLELSDNRISGGLEVLA
          L...VK..VLDN.RS.EG.IEGLTDE.EELE.LS.IN.G.TSVANLPKL.K.KKLELS..RISGGLEVLA
Retrocopy LSRKVKGPVLDNFRSVEGQIEGLTDESEELELLSIINAGFTSVANLPKLDKHKKLELSSKRISGGLEVLA

Parental  EKCPNLTHLNLSGNKIKDLSTIEPLK-KLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDGYDRDDK
          EKC.NLTHLNLSGNKIK.LSTIEPLK.K.ENLKSLDLFN...TNL.DYRENV..LLPQLTYLDG...D..
Retrocopy EKCLNLTHLNLSGNKIKGLSTIEPLK<KSENLKSLDLFNRKLTNLKDYRENVLRLLPQLTYLDGLRPDGQ

Parental  EAPDSDAEGYVEG
          EAPDSDA.G.VEG
Retrocopy EAPDSDA*GDVEG

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_679 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305, retro_cjac_3799,
Dipodomys ordii	ENSDORG00000008611	1 retrocopy	retro_dord_240,
Homo sapiens	ENSG00000140350	3 retrocopies	retro_hsap_1479, retro_hsap_3117, retro_hsap_48,
Gorilla gorilla	ENSGGOG00000015417	1 retrocopy	retro_ggor_1134,
Loxodonta africana	ENSLAFG00000022560	1 retrocopy	retro_lafr_679 ,
Loxodonta africana	ENSLAFG00000026778	1 retrocopy	retro_lafr_580,
Macaca mulatta	ENSMMUG00000022717	1 retrocopy	retro_mmul_1985,
Nomascus leucogenys	ENSNLEG00000013347	2 retrocopies	retro_nleu_15, retro_nleu_2383,
Pongo abelii	ENSPPYG00000006595	2 retrocopies	retro_pabe_210, retro_pabe_2575,
Pan troglodytes	ENSPTRG00000007219	2 retrocopies	retro_ptro_2108, retro_ptro_758,
Rattus norvegicus	ENSRNOG00000045651	1 retrocopy	retro_rnor_1043,
Sarcophilus harrisii	ENSSHAG00000010906	1 retrocopy	retro_shar_540,