RetrogeneDB ID: retro_lafr_1063

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_63:13037949..13038662(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000010897
• Aliases: None
• Description: None

Sequence

>retro_lafr_1063
GTTGCAGCCTGGCTGAAAAAAAATATTTGGAGATCATCCCATTCCACAATATGAGGTGACTCTGTGGACCACAGAGATTT
TGTATCATCTTTCATAATGCAACAAAGCTTGGGACAGGGATGTCTCCCTGGTAATATAGGATTTGAAACAGAAAGCAATC
GAACGTTAATCAGGAGATAAGCATTTTCAAGACCTTCTCATGGAGAGTGTGAATTTTTCCCCTGTCAGTCTCTCTAATGC
TGGTTCCAAGCATCTGAAAGCTTTGTTTGACATTGCAGTGGTGCTTGAGACAAAGGATGTATCACTTACTAGTTTTATTC
CTACGGTGAATGACATGACCTCTAATCTTTTTTGTACCAAATCCAAAAATGTAGAAACCAGGTTTGAGTTGACAAAACCT
TAAAAAAACCTAACTGAAATTTTAGTATTAGAAAAATGTCTACAAGAGGATCTGAAGAAAGCAGAGCAGCATCTCTCTAG
GAAAAAGGGCAAAAGTTGACCATCGACTTCAGAATATGGACTTTCTAAAAGCAAAATCAGAGGAGTTTAGATTTGGAATC
AAAGCTGCAGAGGAGCAACTCTCAGCCAGAGGCATGGATGCTTCTCCGTCTCACCAGTCACTAGTAGCACTATCAGAGAA
GCCAGCAGAACTAAAACGACAGACTATACCTTTGAGGAAATAATTGGAATCCTATTTATATTGAATGACGAAT

Alignment

ORF - retro_lafr_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.66 %
• Parental protein coverage: 85.25 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAAWL-KKIFGDHPIPQYEVNPRTTEILYHLSERNKARDRDVSLVIEDLKQKASEYESEAKHLQDLLMES
          VAAWL.KKIFGDHPIPQYEV...TTEILYHLS..NKA.DRDVSLVI.DLKQKA.E..S..KH.QDLLMES
Retrocopy VAAWL>KKIFGDHPIPQYEVTLWTTEILYHLS*CNKAWDRDVSLVI*DLKQKAIER*SGDKHFQDLLMES

Parental  VNFSPANLSSAGSRYLNALVDIALVLETKDTSLTSFIPAVNDLTSDLFHTKSKNEEIKLELTKLENNLTG
          VNFSP..LS.AGS..L.AL.DIA.VLETKD.SLTSFIP.VND.TS.LF.TKSKN.E...ELTK...NLT.
Retrocopy VNFSPVSLSNAGSKHLKALFDIAVVLETKDVSLTSFIPTVNDMTSNLFCTKSKNVETRFELTKP*KNLTE

Parental  TLVLEKRLQEDLKKAEQHLST-ERARVNHRLQNMDFLKAKSEEFRFRIKAAEEQLSARGMDVSLSHQSLV
          .LVLEK.LQEDLKKAEQHLS...RA.V.HRLQNMDFLKAKSEEFRF.IKAAEEQLSARGMD.S.SHQSLV
Retrocopy ILVLEKCLQEDLKKAEQHLSR>KRAKVDHRLQNMDFLKAKSEEFRFGIKAAEEQLSARGMDASPSHQSLV

Parental  ALSEKLAELKRQTIPLKKKLESYLDLMPN
          ALSEK.AELKRQTIPL.K.LESYL..M.N
Retrocopy ALSEKPAELKRQTIPLRK*LESYLY*MTN

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_1063 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 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001139	3 retrocopies	retro_chof_237, retro_chof_2496, retro_chof_255,
Homo sapiens	ENSG00000152240	3 retrocopies	retro_hsap_3247, retro_hsap_4075, retro_hsap_4655,
Gorilla gorilla	ENSGGOG00000010098	2 retrocopies	retro_ggor_2210, retro_ggor_2888,
Loxodonta africana	ENSLAFG00000010897	1 retrocopy	retro_lafr_1063 ,
Macaca mulatta	ENSMMUG00000003124	2 retrocopies	retro_mmul_2043, retro_mmul_2476,
Monodelphis domestica	ENSMODG00000003208	1 retrocopy	retro_mdom_743,
Nomascus leucogenys	ENSNLEG00000011216	3 retrocopies	retro_nleu_1091, retro_nleu_1698, retro_nleu_2043,
Pongo abelii	ENSPPYG00000009131	3 retrocopies	retro_pabe_2693, retro_pabe_3344, retro_pabe_3615,
Pan troglodytes	ENSPTRG00000009992	3 retrocopies	retro_ptro_2195, retro_ptro_2762, retro_ptro_3092,
Tupaia belangeri	ENSTBEG00000010911	4 retrocopies	retro_tbel_1209, retro_tbel_1348, retro_tbel_3868, retro_tbel_4672,