RetrogeneDB ID: retro_lafr_486

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_19:28795427..28795833(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FGFR1OP2
• Ensembl ID: ENSLAFG00000012476
• Aliases: None
• Description: None

Sequence

>retro_lafr_486
ATGAACTGCACAATTGAGAAGGGATTTGCTGATGCCATAGCTCTTGTGGAAAGACTGAGAAATTCCACAATGCAACACTA
TCTCCTACTACCAAAACTACAGCTCTCATCAAGTGAGTAGAAGTGATGAAGCAGGTTCAGGAAGAAATTCGAAAATAAAA
TAAAGTTGTAAGACATTGACCACGGTTCACAACAGTAACAGGAATCTGTCAAGAAAACAGAAAAATCAAAGACATGTATC
AAATTAATAGAAAATGATGGGCCTTCCTGGAAAAACATCAATCTGCACAGGAATTTATAATGAGCAAATACTGGAAACAA
ATGTTTAAGTTGTTAATGGCTACCAAAATGATTTTGATATAATAATGAAATTAAGAAAGCACCACTCCAAGGTTGACATG
GTACAT

Alignment

ORF - retro_lafr_486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.83 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSCTIEKALADAKALVERLRDHD-DAAESLIEQTTALNKRVEAMKQYQEEIQELNEVARHRPRSTLVMGI
          M.CTIEK..ADA.ALVERLR.....A..S....TTAL.K.VE.MKQ.QEEI...N.V.RH.PR.T.V.GI
Retrocopy MNCTIEKGFADAIALVERLRNST<NATLSPTTKTTALIK*VEVMKQVQEEIRK*NKVVRH*PRFTTVTGI

Parental  QQENRQIRELQQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKK-DDPGIIMKLKEQHSKIDMVH
          .QENR.I....Q.N......LE.HQSA.E.IMSKY..QMF..L....K..D..IIMKL...HSK.DMVH
Retrocopy CQENRKIKDMYQINRK*WAFLEKHQSAQEFIMSKYWKQMFK-LLMATK<NDFDIIMKLRKHHSKVDMVH

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_486 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006966	2 retrocopies	retro_dnov_2342, retro_dnov_2594,
Equus caballus	ENSECAG00000016890	1 retrocopy	retro_ecab_988,
Homo sapiens	ENSG00000111790	1 retrocopy	retro_hsap_994,
Loxodonta africana	ENSLAFG00000010502	1 retrocopy	retro_lafr_565,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486 ,
Monodelphis domestica	ENSMODG00000016618	2 retrocopies	retro_mdom_1788, retro_mdom_244,
Mus musculus	ENSMUSG00000040242	2 retrocopies	retro_mmus_3669, retro_mmus_720,
Pongo abelii	ENSPPYG00000004375	1 retrocopy	retro_pabe_839,
Pan troglodytes	ENSPTRG00000004783	1 retrocopy	retro_ptro_756,
Tupaia belangeri	ENSTBEG00000011581	2 retrocopies	retro_tbel_3732, retro_tbel_4608,