RetrogeneDB ID: retro_lafr_662

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_3:44431728..44432108(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM2D1
• Ensembl ID: ENSLAFG00000013979
• Aliases: None
• Description: None

Sequence

>retro_lafr_662
ACACAGCTCGTTTCATGTTTTCCAACACCCAGCATAGCTCGTAAGGATTTCAGTGGCAATGAAACACATTTTACTGGAAG
TGAAGTTGATTTTCTCAGGCTCACATCTTGTGGAAATGTAAAGGGCTATTCATACAAAATGGCAGTTACTCTTGTCTTTT
TTTTCTTGGATGGCTGGGAGTAGATCTATTTTACCTTGGATACCCTGCCTGGGGTTTGTTAAAGTTTTATACTGGAGGGC
TTCGTGGAATTGGGAGCCTAATTGATTTCATTCTTATTTCAGTGCATATTGTTGGACCTTCAGATGGAAGAAGTTACGTT
ATAGATTACCATGGAACCAGATCGAGCATTACTAACAAAATAGTTAGAAAAACAGTATTA

Alignment

ORF - retro_lafr_662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.6 %
• Parental protein coverage: 63.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TAHVLCFPAPNITCKDFSGNETHFTGNEVGFLKPISCRNVNGYSYKVAVA-LSLFLGWLGADRFYLGYPA
          T..V.CFP.P.I..KDFSGNETHFTG.EV.FL...SC.NV.GYSYK.AV..LS.F....G........P.
Retrocopy TQLVSCFPTPSIARKDFSGNETHFTGSEVDFLRLTSCGNVKGYSYKMAVT>LSFFSWMAGSRSILPWIPC

Parental  LG-LLKFCTVGFCGIGSLIDFILISMQIVGPSDGSSYIIDYYGTRLTRLSITNETFRKTQL
          LG.LLKF.T.G..GIGSLIDFILIS..IVGPSDG.SY.IDY.GTR....SITN...RKT.L
Retrocopy LG>LLKFYTGGLRGIGSLIDFILISVHIVGPSDGRSYVIDYHGTR---SSITNKIVRKTVL

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_662 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011705	1 retrocopy	retro_amel_1290,
Canis familiaris	ENSCAFG00000018838	1 retrocopy	retro_cfam_1213,
Choloepus hoffmanni	ENSCHOG00000013535	1 retrocopy	retro_chof_1494,
Cavia porcellus	ENSCPOG00000012287	1 retrocopy	retro_cpor_471,
Equus caballus	ENSECAG00000015035	1 retrocopy	retro_ecab_556,
Erinaceus europaeus	ENSEEUG00000001567	1 retrocopy	retro_eeur_708,
Loxodonta africana	ENSLAFG00000013979	1 retrocopy	retro_lafr_662 ,
Mus musculus	ENSMUSG00000028563	2 retrocopies	retro_mmus_1412, retro_mmus_1981,
Rattus norvegicus	ENSRNOG00000007527	1 retrocopy	retro_rnor_1104,
Tupaia belangeri	ENSTBEG00000002089	3 retrocopies	retro_tbel_1156, retro_tbel_1730, retro_tbel_201,