RetrogeneDB ID: retro_lafr_497

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:2330101..2330556(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPC25
• Ensembl ID: ENSLAFG00000004668
• Aliases: None
• Description: None

Sequence

>retro_lafr_497
AAAAAGAACACTGAATGGTTGAGATATTTTCTAGAGTATCAAAATTAGCTCTGCAGGCAGAATAAACTCATTCAGGAAAA
AAAAGATAACCTGTTAAAGCTGACTGCTGAAGTAAAATGCAAAAAGTAGGAAATGGAAGTACTGACTGCAAATATCCAGT
ATCTTAAGGAAGAATATGCTGAAAAGAAGGAAATTATATCTATTGTTAACAAAGCTAATGAAACAGGGTGGAAAAGACTG
CAGAAATCTGTATACTTGTATAAAGATCAAATTGGATCAGAAAGTTTATTTTATGATGATAAATTGCAATTTATATTCAC
TAATATTGACCTTAAGCATCCTGAGAGCCCATTTATGTTTTCTCTGCACCTGAATGAAGCAAGGAACTATGAAGTATCAG
ATAGCCATCTTGAGTTCTAGCAGAATTTCAAGAGAATGTAAAGAAGATCAACAAT

Alignment

ORF - retro_lafr_497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.87 %
• Parental protein coverage: 68.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEEDRMIEMFLEYQNQICRQNKHIQEKKDNLLKLIAEVRCKKQEIEVLAANIQDLKEEYAKKKEIISTAN
          K........FLEYQN..CRQNK.IQEKKDNLLKL.AEV.CKK.E.EVL.ANIQ.LKEEYA.KKEIIS..N
Retrocopy KKNTEWLRYFLEYQN*LCRQNKLIQEKKDNLLKLTAEVKCKK*EMEVLTANIQYLKEEYAEKKEIISIVN

Parental  KAIEERLKRLQKSEDLYKYRLGLEIRKIYGDKLQFIFTNIDPKHPESPFVFSLHLNEARDYEVLDSSPHL
          KA.E...KRLQKS..LYK...G.E....Y.DKLQFIFTNID.KHPESPF.FSLHLNEAR.YEV.DS..HL
Retrocopy KANETGWKRLQKSVYLYKDQIGSE-SLFYDDKLQFIFTNIDLKHPESPFMFSLHLNEARNYEVSDS--HL

Parental  E-GLAELQENLRKTNN
          E..LAE.QEN..K.NN
Retrocopy E<VLAEFQENVKKINN

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_497 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013303	4 retrocopies	retro_chof_1070, retro_chof_1541, retro_chof_2326, retro_chof_744,
Cavia porcellus	ENSCPOG00000005926	1 retrocopy	retro_cpor_1032,
Dasypus novemcinctus	ENSDNOG00000004429	1 retrocopy	retro_dnov_826,
Echinops telfairi	ENSETEG00000015642	1 retrocopy	retro_etel_1554,
Loxodonta africana	ENSLAFG00000004668	1 retrocopy	retro_lafr_497 ,
Monodelphis domestica	ENSMODG00000007753	1 retrocopy	retro_mdom_1828,
Tupaia belangeri	ENSTBEG00000012559	1 retrocopy	retro_tbel_2798,
Tursiops truncatus	ENSTTRG00000006112	1 retrocopy	retro_ttru_574,