RetrogeneDB ID: retro_lafr_817

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:64626368..64626941(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LMX1B
• Ensembl ID: ENSLAFG00000015481
• Aliases: None
• Description: None

Sequence

>retro_lafr_817
ATGCTGGACGGCATCAAGATGGAGGAGCACGCCCTGGGCCCCGAGCTTGCCACTCTAGGGGTGCTGCTGGGCTCTGACTG
CCCGCATCCCGCTGTCTGCTAGGGCTACCAGCGGCCCATCTCCGACCGCTTCCTGACGCCAGTCAACCAGTCGTCCTGGC
ACGAGGAGGGTTTGCCGTGTACGGCCTGTCAGCAAGCCCTCACCACCAGCTGCTCCTTCCGGGAGCCGAAACCGACTGCT
GACAAGACTACCGACAGCTCTTCACTGCCAAGTGCAGCGGCTGCTCGGAGAAGATTGCACCCACCAAGTTCGTGACGCGG
GCGCTGGAATGCGTGTATCACCTGGGCTGCTTCTGCTGCTGCGTGTGTGAGCGGCAGCTACACAAGGGCAGTGCGTTTGT
GCTTAAGGAGGGCCAGCTACTGTGCAAAGGGTGATTACTGGGAGGTGAAGGACCTGCTCAGCTTCGTGAGCCCCAACGAG
TCTGACTCTGGCCAGGTTGTGTCCCCTATAGTGAAGAGTGCGGACGAGGATGGAGACATGAAGCAGGCCAAGGGGCAGGG
CAGCCAAAGCAAG

Alignment

ORF - retro_lafr_817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.02 %
• Parental protein coverage: 51.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLDGIKMEEHALRPGPATLGVLLGSDCPHPAVCEGCQRPISDRFLMRVNESSWHEECLQCAACQQALTTS
          MLDGIKMEEHAL.P..ATLGVLLGSDCPHPAVC.G.QRPISDRFL..VN.SSWHEE.L.C.ACQQALTTS
Retrocopy MLDGIKMEEHALGPELATLGVLLGSDCPHPAVC*GYQRPISDRFLTPVNQSSWHEEGLPCTACQQALTTS

Parental  CYFRDRK-LYCKQDYQQLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQ
          C.FR..K...C.QDY.QLF.AKCSGC.EKIAPT.FV.RALECVYHLGCFCCCVCERQL.KG..FVLKEGQ
Retrocopy CSFREPK<TDC*QDYRQLFTAKCSGCSEKIAPTKFVTRALECVYHLGCFCCCVCERQLHKGSAFVLKEGQ

Parental  LLC-KGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGK
          LLC.KGDY...KDLLS.VSP.ESDS..............G...Q.KG.G...K
Retrocopy LLC>KGDYWEVKDLLSFVSPNESDSGQVVSPIVKSADEDGDMKQAKGQGSQSK

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_817 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000015481	1 retrocopy	retro_lafr_817 ,