RetrogeneDB ID: retro_lafr_1043

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_60:8077008..8077325(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSLAFG00000001021
• Aliases: None
• Description: None

Sequence

>retro_lafr_1043
CTACAGTTTTTAGGATTATATAAGAAAAGTGGTAAATTGGAATTTCTTGGATTGGATAACGCGGGAAAAACACCACCACT
ACACTCGCTACAAAATGACAGACTTGGATAGCGTGTTCCAACGTTATACCCCTCTTCAGAAGAACTGGCCATTGCTGGTA
TGACTTTTACAACTTTTGATCTGGATGGACATGTTCAAGCCTAAAGAATGTGGAAAAACTACCTTCCTGCTATCAATGGC
AGCATACTTCTGATGGATTGTGCGGACCACGAAAGGCTGTTAGACTCAAAAGAGGACCTTGTTCACTAATGACAGAT

Alignment

ORF - retro_lafr_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.5 %
• Parental protein coverage: 53.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHVQARRV
          LQFLGLYKK.GKL.FLGLDNAGKT..LH.L..DRLG..VPTL.P.SEEL.IAGMTFTTFDL.GHVQA.R.
Retrocopy LQFLGLYKKSGKLEFLGLDNAGKTPPLHSLQNDRLG*RVPTLYPSSEELAIAGMTFTTFDLDGHVQA*RM

Parental  WKNYLPAINGIVFLVDCADHERLLESKEEL-DSLMTD
          WKNYLPAING...L.DCADHERLL.SKE.L..SLMTD
Retrocopy WKNYLPAINGSILLMDCADHERLLDSKEDL<CSLMTD

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_1043 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017849	1 retrocopy	retro_amel_1075,
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804, retro_dnov_919,
Equus caballus	ENSECAG00000012409	1 retrocopy	retro_ecab_948,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043 ,
Macaca mulatta	ENSMMUG00000004417	3 retrocopies	retro_mmul_1825, retro_mmul_2507, retro_mmul_304,
Oryctolagus cuniculus	ENSOCUG00000008250	1 retrocopy	retro_ocun_1004,
Otolemur garnettii	ENSOGAG00000013347	1 retrocopy	retro_ogar_2472,
Pteropus vampyrus	ENSPVAG00000012433	2 retrocopies	retro_pvam_1219, retro_pvam_725,
Ictidomys tridecemlineatus	ENSSTOG00000011326	1 retrocopy	retro_itri_1714,
Tursiops truncatus	ENSTTRG00000016864	2 retrocopies	retro_ttru_1225, retro_ttru_857,