RetrogeneDB ID: retro_lafr_587

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:15113016..15113581(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND6
• Ensembl ID: ENSLAFG00000006722
• Aliases: None
• Description: None

Sequence

>retro_lafr_587
ATCACTCAAGAAACTAATCACAGCCAAGTGCCTGTGCTTTGTTCCACTGGCTGAGGATTTTATGGAAATCCTTGTACAAA
TGGCATGCATTCGGTATGCTATAAGGGACATCTTCAAAGACAGAATAGTGGTAATGGTAGAAGAAGCCCATCTGAAACTT
GTCAGTAGTTTGTCTGAATCTTTACAACTTCAGTGGACAGATGGCAGTGTCCCAGACGTTCAGTCATCTTTAGTCCCTAA
GTCTTCATCTATGCAGCCAAGCCCTGTACCAAATTAGTCACTTTTATCAGAATATGTAGCTTCTTCTCAGGTGGACAGTG
GATCTCTGAACAATGCAACACCTGAAACAGAAGACCTGCAAGGCCTCAAAGCAGCGAGCATTGTTCCTCTTGAATGTGAT
TTTCCATCTTCAGCACCAGATACCCCAGAACAACCATCTGAAGGGCAAAACAAGTCTCTTGGAAAACAAAAGAGGAATCA
CCATTTCATATGCTGAAAGAAAGTGGGACTTACTGGGTTTGAATGCCAATGTGGAAATGTGTACATCGTTACTCAGATGT
ACACA

Alignment

ORF - retro_lafr_587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.88 %
• Parental protein coverage: 85.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQETNHSQVPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQNSSNGRISPPATS-VSSLSESLPVQCTDG
          ..QETNHSQVP.LCSTG.GFYGNP.TNGM.SVCYK.HLQRQNS.NGR.S.P....VSSLSESL..Q.TDG
Retrocopy ITQETNHSQVPVLCSTG*GFYGNPCTNGMHSVCYKGHLQRQNSGNGRRS-PSET>VSSLSESLQLQWTDG

Parental  SVPEAQSSLDFTSSSMQPSPVSNQSLLSESVASSQVDSTSLDKAAPETEDLQGPRAEGLVPLECDPPSSV
          SVP..QSSL...SSSMQPSPV.N.SLLSE.VASSQVDS.SL..A.PETEDLQG..A...VPLECD.PSS.
Retrocopy SVPDVQSSLVPKSSSMQPSPVPN*SLLSEYVASSQVDSGSLNNATPETEDLQGLKAASIVPLECDFPSSA

Parental  PDTAQQPSEEQNKSLEKPKQKKNRCFMCRKKVGLTGFECRCGNVYCGVHRYS
          PDT..QPSE.QNKSL...KQK.N..F.C.KKVGLTGFEC.CGNVY.....Y.
Retrocopy PDTPEQPSEGQNKSL--GKQKRNHHFIC*KKVGLTGFECQCGNVYIVTQMYT

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_587 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012321	1 retrocopy	retro_btau_593,
Choloepus hoffmanni	ENSCHOG00000009491	2 retrocopies	retro_chof_1516, retro_chof_2072,
Felis catus	ENSFCAG00000012931	2 retrocopies	retro_fcat_1024, retro_fcat_1998,
Homo sapiens	ENSG00000086666	1 retrocopy	retro_hsap_4153,
Gorilla gorilla	ENSGGOG00000015621	1 retrocopy	retro_ggor_2790,
Loxodonta africana	ENSLAFG00000006722	1 retrocopy	retro_lafr_587 ,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685,
Nomascus leucogenys	ENSNLEG00000008870	1 retrocopy	retro_nleu_1387,
Pan troglodytes	ENSPTRG00000007361	2 retrocopies	retro_ptro_1375, retro_ptro_2824,
Rattus norvegicus	ENSRNOG00000013506	1 retrocopy	retro_rnor_2019,
Sus scrofa	ENSSSCG00000001779	2 retrocopies	retro_sscr_1206, retro_sscr_1207,