RetrogeneDB ID: retro_lafr_365

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_130:2141948..2142382(+)
• Located in intron of: ENSLAFG00000011299

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19ORF40
• Ensembl ID: ENSLAFG00000006401
• Aliases: None
• Description: None

Sequence

>retro_lafr_365
TATATCACTGCAGCTGATTTGGTGGCAGGAAATGGCTACAGAAAGAGGCTTGTTCAGGTTAGAAATTCCAGTAATCTTCA
AGGGATTGTACCAGTTGAAAAGATAGAGATGAGTGAACAATACTTTCCAGCTGTACAGAAGTTTACTGTGCTGGGCGCCT
TGGGATGGTGTTGCTTCCAGTGGCCAGGCAGATGGAAGCATCCTGCCTCATTATCCGCTTAATTCAAGAGCAAACCAAAA
AGCTCAATGAGAACACTTCTCTCAGGAAGACACATTCTCTGCTCTCTGAGCCATCCCTCCTGTGAACTGTGTAGCAGGTC
CCAGGAGTTGGAAAAGTTAAAGCTCCCATTCTGCTTCAAAAATTCCCAAGTATCCAACAACTAAGTAACGCATCCATGCA
AGAACTTAAGCAAGTCATTGGACAAGGAGTAGCA

Alignment

ORF - retro_lafr_365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.71 %
• Parental protein coverage: 67.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YITEADLVAGNGYRKRLVRVRNSSNLQGIILVEKTQMSEQYFPAVQKFTVLD-LG-MVLLPVASQMEASR
          YIT.ADLVAGNGYRKRLV.VRNSSNLQGI..VEK..MSEQYFPAVQKFTVL..LG.MVLLPVA.QMEAS.
Retrocopy YITAADLVAGNGYRKRLVQVRNSSNLQGIVPVEKIEMSEQYFPAVQKFTVLGALG<MVLLPVARQMEASC

Parental  LIIQLVQEQTKEPSKNPFVRKKCTVLSEPSLLRTVQQIPGVGKVKAPLLLQKFPSIQELSNASIHELEQV
          LII.L.QEQTK....N...RK....LSEPSLL.TV.Q.PGVGKVKAP.LLQKFPSIQ.LSNAS..EL.QV
Retrocopy LIIRLIQEQTKKLNENTSLRKTHSLLSEPSLL*TV*QVPGVGKVKAPILLQKFPSIQQLSNASMQELKQV

Parental  VGQAVA
          .GQ.VA
Retrocopy IGQGVA

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_365 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000728	2 retrocopies	retro_cjac_1011, retro_cjac_3952,
Cavia porcellus	ENSCPOG00000011965	1 retrocopy	retro_cpor_1536,
Dasypus novemcinctus	ENSDNOG00000014134	4 retrocopies	retro_dnov_1817, retro_dnov_2382, retro_dnov_426, retro_dnov_942,
Echinops telfairi	ENSETEG00000002716	1 retrocopy	retro_etel_458,
Loxodonta africana	ENSLAFG00000006401	4 retrocopies	retro_lafr_165, retro_lafr_365 , retro_lafr_415, retro_lafr_789,
Myotis lucifugus	ENSMLUG00000013287	1 retrocopy	retro_mluc_522,
Macaca mulatta	ENSMMUG00000017939	1 retrocopy	retro_mmul_788,
Procavia capensis	ENSPCAG00000009727	1 retrocopy	retro_pcap_444,
Sarcophilus harrisii	ENSSHAG00000016372	1 retrocopy	retro_shar_299,