RetrogeneDB ID: retro_lafr_383

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_14:14208766..14209612(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBS
• Ensembl ID: ENSLAFG00000009950
• Aliases: None
• Description: None

Sequence

>retro_lafr_383
GACACCACTACTAAGGAGATACTACAGCAGTATGATGGGAAATTGGACATGCTGCTGGCTTCAGGGGACATGGGCGGCAC
CATCATGGGCATTGCCAAAAATCTCAAGGAGAAGTGTGCTGGGTGCAGAACCACTGAGATGGATCCCAAGGGGCTCATTG
TTGCAGAACCAGGAAGGCTCCATCAGACAGAGCAGATGACCTGTGAAGTAGAGGGATTGACTGTGACATCATCCTCATGG
TGCTGGACAGGATGCTGGTGGGCAAGTGGTTCAGAAGCAACGACAAGGAGTCCTTACCCTTTCCCCCATGGCGAATGACC
AGGAGGGGCTACTGTGTGGTGGTAATGCGAGCATCACCATGTCCATCACTGTGAACGGCCGCCAGGAGCTGCAGGGGGGC
CTGCGCTGCATCATCATTTTGTTCGGCTCTGTGAGGAGCTACATTTCCAAGTTCCTGAGCACCAGGTGGGTACTATCAAA
GGGTTTCATGGAGAAGGAACATTGTGGTTGAAGAAGCCATGGTGGTAGCAACTCAGAGTTCAGGAAATGAGTCTGCCGGC
CTTGCTGACAGTGCTGCCAAAGGTCACCTGTGAACACACTACTGAGATCCTTTGAGAGAAGGGCTCTGACCAGGCATCTG
TAGTCAGTGAGTTGGGGGTAGTCCTGGGGATCACTCTTGGGAACATGCTGCAGTCCCTGCTCACCAGAAGGTTCAGCCTT
AAGAATCAAGTCCACAAAGTTATTTACAAGCAGTTCAAACAGATCATTCCGACATCCCCACTGGGCAAGCTGTCGTACAT
CCTGGAGGTGGACCACTTTGGTCTGGTGATCCGCAAGCAGATCCAG

Alignment

ORF - retro_lafr_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.37 %
• Parental protein coverage: 50.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DTTAEEILQQCDGKLDMLVASAGTGGTITGIARKLKEKCPGCKIIGVDPEGSILAEPEELNQTDQTAYEV
          DTT..EILQQ.DGKLDML.AS...GGTI.GIA..LKEKC.GC.....DP.G.I.AEP..L.QT.Q...EV
Retrocopy DTTTKEILQQYDGKLDMLLASGDMGGTIMGIAKNLKEKCAGCRTTEMDPKGLIVAEPGRLHQTEQMTCEV

Parental  E-GIGYDFLPTVLDRTVVDKWFKSNDEDSFAF-ARMLIAQEGLLCGGSAGSTMSIAVKAAQELQEGQRCV
          E.GI..D....VLDR..V.KWF.SND..S..F...M...QEGLLCGG.A..TMSI.V...QELQ.G.RC.
Retrocopy E<GIDCDIILMVLDRMLVGKWFRSNDKESLPF<SPMANDQEGLLCGGNASITMSITVNGRQELQGGLRCI

Parental  VILPDSVRNYMSKFLSDRWMLQKGFMKEE-DMVVKKPWWWHLRVQELSLSAPLTVLPTVTCEHTIEILRE
          .IL..SVR.Y.SKFLS.RW.L.KGFM..E.....KKPWW..LRVQE.SL.A.LTVLP.VTCEHT.EIL.E
Retrocopy IILFGSVRSYISKFLSTRWVLSKGFMEKE<TLWLKKPWW*QLRVQEMSLPALLTVLPKVTCEHTTEIL*E

Parental  KGFDQAPVVDEAGMILGMVTLGNMLSSLLAGKVQPSDQVRKVIYKQFKQIRLTDPLGQLSHILEMDHFAL
          KG.DQA.VV.E.G..LG..TLGNML.SLL........QV.KVIYKQFKQI..T.PLG.LS.ILE.DHF.L
Retrocopy KGSDQASVVSELGVVLG-ITLGNMLQSLLTRRFSLKNQVHKVIYKQFKQIIPTSPLGKLSYILEVDHFGL

Parental  VVHEQIQ
          V...QIQ
Retrocopy VIRKQIQ

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_383 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000009950	1 retrocopy	retro_lafr_383 ,
Oryzias latipes	ENSORLG00000008831	1 retrocopy	retro_olat_55,
Sarcophilus harrisii	ENSSHAG00000017100	1 retrocopy	retro_shar_587,