RetrogeneDB ID: retro_lafr_906

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_48:2606173..2606462(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM12
• Ensembl ID: ENSLAFG00000005202
• Aliases: None
• Description: None

Sequence

>retro_lafr_906
GAGAAGGAGAAGCTGAGCCAGGCGTATGCTGTTGGCCCCGCCGTCTCCCTAGAGGGCCCGCAGCTCTTCCAGACCATTCA
CAAGACCAATAAAGACGGCAAATAACGAGGAAAAAAACGTAGCCCTGGAAGAATTTGTTATTACAACCACCCCTTCCCCA
TGTAAGTGGCAAAGTGAGGGGAGAGCACTACACAAAATAGTTGGAAAATGCTTCAGAGACATGGAAAGCCAAAAGATACT
GCAGCATTCGCAAGCACGGCAACCACGGAAGAAGGCTTCTCTGTCATCA

Alignment

ORF - retro_lafr_906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.19 %
• Parental protein coverage: 51.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCK-WQEKNIVVMEEVVITPPYQVENCKGK-EGSALSHV
          ..EKLSQAYA....VSLEG.QLFQTIHKT.KD.K...EKN....E.V..T.P.....CK...EG.AL...
Retrocopy EKEKLSQAYAVGPAVSLEGPQLFQTIHKTNKDGK>NEEKNVALEEFVITTTP---SPCKWQSEGRAL---

Parental  RKIVEKHFRDVESQKILQRSQAQQPQKEAALSS
          .KIV.K.FRD.ESQKILQ.SQA.QP.K.A.LSS
Retrocopy HKIVGKCFRDMESQKILQHSQARQPRKKASLSS

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_906 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843, retro_cfam_312,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906 ,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,