RetrogeneDB ID: retro_lafr_875

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_42:19132437..19133296(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGK1
• Ensembl ID: ENSLAFG00000012698
• Aliases: None
• Description: None

Sequence

>retro_lafr_875
TTCATGAAACAGAGGAGGATGGATCCGAATGACTTTATTCAGAAGATTGCCAACAACTCCTATGCATGCAAGCACTCTGG
AGTCCAGTCTGTTTTAAAAATCTCCCAAACTCAAGAGCCTGAGCTTATGAATGCAGATTCTTTTCCACAAAGTCCTTCTC
AGCAAAGCAACTTTGGCTCATTGTCCAACCCTCATGTGAAGGCATTCCACTTTCACTTCTTGAAAGTAATTGGAAAAGGT
GGTTTTGGAAAGGTTTTTCTAGCAAGACACAAGGCAGAAGAAGCATTCTAGTCAGTCTACGTTCTACAAAAGAAAACATT
CCTGAAAAAGGAAGAGGAGAAGCATATAATGTTAAAGAAGAATGTTCTACTGGAAAATGTGAAACATCATTTCTGGGTGG
GCCTTCACTTCCCTTTCCAGGCTGCTGAAAAATTAAACTTTGTCCTAGACTACATTAACAGTGGAGAATGCTTTTCCACC
TCCAGAGGGAGTCCTCGCTTGAATCATGGGCTCCTTTTTATGCCGACGAAACATCCAGAGCCTTGGGTTACCTGCACTCT
CTGAATATCATTTACAGAGACTTAAAACCAGAGAATATTATACTAGATTCACAGGGACACATTGTCCTAACTTACTTTGG
GCTCTGCAAGGAGAACGTTGAACACAACGGAACGATATCCACCTTCTGTGGCACACTTGAGTATTTGGCCCCAGAAGTGC
TTAATAGAAGTCTTACAACAAAACCATAGACTGGTGGTACCTGGGGAGCCTTTTGTATAAATGCTATATGGCCTGCCTCC
TTTTTTACAGCCAAAATATTGCTAACATGTACCACGACATTCTGAACAATCCCCTGCAG

Alignment

ORF - retro_lafr_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.04 %
• Parental protein coverage: 55.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FMKQRRMGLNDFIQKIANNSYACKHPEVQSILKISQPQEAEFMNANPSPPPSPSQQINLGPSSNPHAKPS
          FMKQRRM..NDFIQKIANNSYACKH..VQS.LKISQ.QE.E.MNA..S.P.SPSQQ.N.G..SNPH.K..
Retrocopy FMKQRRMDPNDFIQKIANNSYACKHSGVQSVLKISQTQEPELMNAD-SFPQSPSQQSNFGSLSNPHVKAF

Parental  DFHFLKVIGKGSFGKVLLARHKAEEVFYAVKVLQKKAILKKKEEKHIMSERNVLLKNVKHPFLVGLHFSF
          .FHFLKVIGKG.FGKV.LARHKAEE.F..V.VLQKK..LKK.EEKHIM...NVLL.NVKH.F.VGLHF.F
Retrocopy HFHFLKVIGKGGFGKVFLARHKAEEAF*SVYVLQKKTFLKKEEEKHIMLKKNVLLENVKHHFWVGLHFPF

Parental  QTADKLYFVLDYINGGELF-YHLQRERCFLEPRARFYAAEIASALGYLHSLNIVYRDLKPENILLDSQGH
          Q.A.KL.FVLDYIN.GE.F..HLQRE...LE..A.FYA.E...ALGYLHSLNI.YRDLKPENI.LDSQGH
Retrocopy QAAEKLNFVLDYINSGECF<FHLQRESS-LESWAPFYADETSRALGYLHSLNIIYRDLKPENIILDSQGH

Parental  IVLTDFGLCKENIEHNGTTSTFCGTPEYLAPEVLHK-QPYDRTVDWWCLGAVLYE-MLYGLPP-FYSRNT
          IVLT.FGLCKEN.EHNGT.STFCGT.EYLAPEVL.....Y..T.DWW.LG..LY..MLYGLPP.FYS.N.
Retrocopy IVLTYFGLCKENVEHNGTISTFCGTLEYLAPEVLNR<KSYNKTIDWWYLGSLLYK<MLYGLPP>FYSQNI

Parental  AEMYDNILNKPLQ
          A.MY..ILN.PLQ
Retrocopy ANMYHDILNNPLQ

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_875 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006626	1 retrocopy	retro_chof_2212,
Erinaceus europaeus	ENSEEUG00000008758	1 retrocopy	retro_eeur_564,
Loxodonta africana	ENSLAFG00000012698	1 retrocopy	retro_lafr_875 ,
Microcebus murinus	ENSMICG00000007886	1 retrocopy	retro_mmur_401,
Oryctolagus cuniculus	ENSOCUG00000014367	1 retrocopy	retro_ocun_1114,
Tursiops truncatus	ENSTTRG00000009699	1 retrocopy	retro_ttru_22,