RetrogeneDB ID: retro_lafr_953

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_50:9173489..9173780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHIC2
• Ensembl ID: ENSLAFG00000012248
• Aliases: None
• Description: None

Sequence

>retro_lafr_953
ATCAACAGAGTTAACAGTTGTCTTAAGAACCTTCCTGTTAACGCATGTTGGCTACTTTGTGGCTTCCTTTGTTGCTGCTG
CACGTTAGGCTGCAGTATGTGGCCAGTTATTTGCCTCAGTAAAAGAGCAAGAACATCGACTGAGAAGTTATTAGAACGGG
AAAACAATAGGTGATACCACAAGCTGTGCTTGCACTGAAGACTGAGGAAAAGGAAATGTGAAATGAATAATGTGATGGAA
TATGTCATCCTCATAGACTTTTTACCAAAGACACCAAGTTTTTGACCAGAT

Alignment

ORF - retro_lafr_953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 59.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  INRVNRCLKKNLPVNVRWLLCGCLCCCCTLGCSMWPVICLSNRTRRSIEKLLEWENNRLYHKLCLHWRLS
          INRVN.CLK.NLPVN..WLLCG.LCCCCTLGCSMWPVICLS.R.R.S.EKLLE.ENNR.YHKLCLH.RL.
Retrocopy INRVNSCLK-NLPVNACWLLCGFLCCCCTLGCSMWPVICLSKRARTSTEKLLERENNR*YHKLCLH*RLR

Parental  KRKCETNNMMEYVILIEFLPKTPIFRPD
          KRKCE.NN.MEYVILI.FLPKTP.F.PD
Retrocopy KRKCEMNNVMEYVILIDFLPKTPSF*PD

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_953 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024493	1 retrocopy	retro_cpor_1448,
Echinops telfairi	ENSETEG00000004296	1 retrocopy	retro_etel_1804,
Latimeria chalumnae	ENSLACG00000006603	1 retrocopy	retro_lcha_22,
Loxodonta africana	ENSLAFG00000012248	1 retrocopy	retro_lafr_953 ,
Macaca mulatta	ENSMMUG00000006382	1 retrocopy	retro_mmul_1372,