RetrogeneDB ID: retro_lafr_713

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_32:19661982..19662874(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A6
• Ensembl ID: ENSLAFG00000001584
• Aliases: None
• Description: None

Sequence

>retro_lafr_713
ATGACGGAACAGGCCATCTCCCTCGCCAAGGTCTTACTGGTGAGCGACATCACAGCCGCCATCTCCAAGACTACCATGGC
CCCAATCGAGCGGGTCAAGCTGTTGCTGCAGGTGCAGCACACCAGCAAGCAGATGGCGGCAGACAAGCCGTACAAGGACA
TCGTGGACTGCACCATGTGCATCCCCAAGGAGGAAGGTGTGCTGTCCTTCCGGCGGGGCAACCTGGCCAACGTCATCCGC
TACTTCCTCATCCAGGCCCTCAACTTCACCTTCAAGGACAAGTACAAGCAGGTCTTCTCGGGCAGTGTGGACAAGCACAC
GCCGTTCTAGCGGTACTTTGCTGGCAAACTGGCCTCTGGAGCGGTGGCCGGCGCCGCCTCCCTCTGCTTAGTCTACCCGC
TGGATTTTGCCAGAACACACCTGGCAGCCGACATCAACAAGTCCAGCACCGAACGGGAATTCAAGGGCCCGGGAAACTGT
TCGGTGAAGGTCACCAAGTCGGACGGCATCCGTGGCCAGTAAAGGGCTTCAACGTGTCCATGTAGAGAGGATTATCATCT
ACCAGGCAGCCTACTTCAGCGTCTACGACATGGCCAAAGGCATGCTCCCCGACCCCAAGGACACACACATCTTGGTCAGC
TGGATGATCACCCAGACCGTGACAGCCGTGGCCGGCGTCGTCTCCTACCCCTTCAACACTGTGCGGTGACGCATGATAAT
GCAGTCGGGGCGCAAAAGAGCCAACATCATGTACACTGGGACCATGTACTGCTGACGGAAGATCTTCAAGGACGAGGGCT
ACAAGGCCTTCTTCACAGGCTGGTCCAACGTGCTGAGGGGCATGTGCGGGGCATTCGTACTGGTCCTCTACAAGGAGCTC
AAAAAGGTCATC

Alignment

ORF - retro_lafr_713 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTEQAISFAKDFLAGGIAAAISKTAVAPIERVKLLLQVQHASKQIAADKQYKGIVDCIVRIPKEQGVLSF
          MTEQAIS.AK..L...I.AAISKT..APIERVKLLLQVQH.SKQ.AADK.YK.IVDC...IPKE.GVLSF
Retrocopy MTEQAISLAKVLLVSDITAAISKTTMAPIERVKLLLQVQHTSKQMAADKPYKDIVDCTMCIPKEEGVLSF

Parental  WRGNLANVIRYFPTQALNFAFKDKYKQVFLGGVDKHTQFWRYFAGNLASGGAAGATSLCFVYPLDFARTR
          .RGNLANVIRYF..QALNF.FKDKYKQVF.G.VDKHT.F.RYFAG.LASG..AGA.SLC.VYPLDFART.
Retrocopy RRGNLANVIRYFLIQALNFTFKDKYKQVFSGSVDKHTPF*RYFAGKLASGAVAGAASLCLVYPLDFARTH

Parental  LAADVGKSGAEREFKGLGDCLVKITKSDGVRGL-YQGFNVSV-QGI-IIYRAAYFGIYDTAKGMLPDPKN
          LAAD..KS..EREFKG.G.C.VK.TKSDG.RG....GFNVS...G..IIY.AAYF..YD.AKGMLPDPK.
Retrocopy LAADINKSSTEREFKGPGNCSVKVTKSDGIRGQ<VKGFNVSM*RGL<IIYQAAYFSVYDMAKGMLPDPKD

Parental  THIVISWMIAQTVTAVAGVVSYPFDTVRRRMMMQSGRKGADIMYTGTIDCWRKIFKDEGGKAFFKGAWSN
          THI..SWMI.QTVTAVAGVVSYPF.TVR.RM.MQSGRK.A.IMYTGT..C.RKIFKDEG.KAFF.G.WSN
Retrocopy THILVSWMITQTVTAVAGVVSYPFNTVR*RMIMQSGRKRANIMYTGTMYC*RKIFKDEGYKAFFTG-WSN

Parental  VLRGMGGAFVLVIYDELKKVI
          VLRGM.GAFVLV.Y.ELKKVI
Retrocopy VLRGMCGAFVLVLYKELKKVI

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_713 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005609	1 retrocopy	retro_amel_255,
Homo sapiens	ENSG00000169100	5 retrocopies	retro_hsap_1207, retro_hsap_150, retro_hsap_2460, retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla	ENSGGOG00000023004	2 retrocopies	retro_ggor_239, retro_ggor_2785,
Loxodonta africana	ENSLAFG00000001584	1 retrocopy	retro_lafr_713 ,
Loxodonta africana	ENSLAFG00000029398	1 retrocopy	retro_lafr_844,
Microcebus murinus	ENSMICG00000006136	2 retrocopies	retro_mmur_1021, retro_mmur_922,
Macaca mulatta	ENSMMUG00000006899	1 retrocopy	retro_mmul_1182,
Nomascus leucogenys	ENSNLEG00000000389	1 retrocopy	retro_nleu_895,
Otolemur garnettii	ENSOGAG00000000963	2 retrocopies	retro_ogar_2492, retro_ogar_2499,