RetrogeneDB ID: retro_lafr_630

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_27:13344965..13345249(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPP21
• Ensembl ID: ENSLAFG00000010777
• Aliases: None
• Description: None

Sequence

>retro_lafr_630
CCTTTGGTGAAGAGGACCCTCTGTCATGGCTGTTCTTCCCTCCTTATCCGGGCCTGTGTTGTACCCAGTGCCAGAGATGC
CGTAAGGGAAGGTACTGGACAGTACAGACCTGCCTAACATGACAGCGTAGCCAACGATTCCTCAACGATCCCTTTCATCT
GCCCTGGGAAGACTGTCCTGGAGCCCTGGTGGGGAGCCAGGCAGATCCCAAACCACCATAGCCCTTGCCAAGCACAGCTC
ACCCCATTCCAGCCCACCTTCCTGAGGAGCAAGTGCACCCTCAG

Alignment

ORF - retro_lafr_630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.12 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSVKRTLCRGCSSLLI-PGLTCTQRQRRRKGQRWTVQTCLTCQRSQRFLNDPRHLLWGDRPEAQLGNQAD
          P.VKRTLC.GCSSLLI.PGL.CTQ.QR.RKG..WTVQTCLT.QRSQRFLNDP.HL.W.D.P.A..G.QAD
Retrocopy PLVKRTLCHGCSSLLI<PGLCCTQCQRCRKGRYWTVQTCLT*QRSQRFLNDPFHLPWEDCPGALVGSQAD

Parental  PKPPQPLPSTAHPIPAHLPEEKVEPR
          PKPP.PLPSTAHPIPAHLPEE.V.P.
Retrocopy PKPP*PLPSTAHPIPAHLPEEQVHPQ

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_630 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012222	1 retrocopy	retro_chof_69,
Loxodonta africana	ENSLAFG00000010777	1 retrocopy	retro_lafr_630 ,
Monodelphis domestica	ENSMODG00000015967	2 retrocopies	retro_mdom_1142, retro_mdom_1340,