RetrogeneDB ID: retro_lafr_594

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:364426..365011(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM133B
• Ensembl ID: ENSLAFG00000029755
• Aliases: None
• Description: None

Sequence

>retro_lafr_594
ATGGGAAAGCGAGATAATCGGGTGGCCTATATGAATCCTGTAGCAATGGCCAGATGGAAGGGCACATCTCCGTACATAGG
GCCAACAATACAAGATTATCTGAATCGGCCAAGACCTACCTGGGAAGAAGTGAAAAAACAACTAGAAAATAAAAAGAAAG
GCTCCAAGGCATTAGCTGAATTTGAAGAAAAAATGAATGAGAATTGGAAGAAAGAACTAGAAAAAAGCAGAGAGAAAATA
TTAAGTGGAAATGTGAGCTCATCTAAAAAAAAAGAAAAAAAGAAAAAGAAAAAGAAGAAATCTTATCGATCTTCATCTTC
TTCATCAAGCTCTGACTCTTCCAGCAGTTCTTCAGATTCTGAGAATGAGGATAAGAGACAAGGGAAAAAGAGAAAGAAAA
AGAAGAATCGTTCCTTCAGATCTTCATACAGCTCTACATCTGAATCAGAGGACAAAGAATCCTTAAAAAAGAAAAAGAAA
TCAAAGGATGAAACAGAGAAGGAAAAGTATATTAGCAAAAAAAGAAAGAAGATCCATTCTGGGGATAAACCTTTATCATC
TGAGTCCTCATCAGAATCAGATTAT

Alignment

ORF - retro_lafr_594 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73. %
• Parental protein coverage: 80.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEKMNENWK
          MGKRDNRVAYMNP.AMAR..G.....GPTIQDYLNRPRPTWEEVK.QLE.KKKGSKALAEFEEKMNENWK
Retrocopy MGKRDNRVAYMNPVAMARWKGTSPYIGPTIQDYLNRPRPTWEEVKKQLENKKKGSKALAEFEEKMNENWK

Parental  KELEKHREKLLSGSESSSKKRQRKKKEKKKSGRYSSSSSSSSDSSSSSSDSEDEDKRQGKRRKKKKNRSH
          KELEK.REK.LSG..SSS............S.R.SSSSSSSSDSSSSSSDSE.EDKRQGK.RKKKKNRS.
Retrocopy KELEKSREKILSGNVSSSXXXXXXXXXXXXSYR-SSSSSSSSDSSSSSSDSENEDKRQGKKRKKKKNRSF

Parental  KSSESSMSGTESDSKDSFKKKKKSKDTTEKEKDIKGLGKKRKLYPEDKPLSAESLSESDY
          .SS.SS.S..ES..K.S.KKKKKSKD.TEKEK.I....K..K....DKPLS.ES.SESDY
Retrocopy RSSYSSTS--ESEDKESLKKKKKSKDETEKEKYIS--KKRKKIHSGDKPLSSESSSESDY

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_594 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 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594 ,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,