RetrogeneDB ID: retro_lafr_142

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:68203527..68204119(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028564
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COMMD10
• Ensembl ID: ENSLAFG00000011885
• Aliases: None
• Description: None

Sequence

>retro_lafr_142
GCTTTGATCGTTCGGGAGACCCCCAGCATGAAAAAAGCAGTGTCGCTGATAAATGCAATAGATACAGGAACATTTCCACA
GTTGCTCACTGGAATTCTTCAAAAATTTCATCTAAAGGCTGAAAGCAGTTTCAGTGAAGAAGAGGAAGAAAAACTTCAAG
CTGTATTTTTCTCTAGAGAAACAAGACCTTCACCTAGTTCTTGAAACAGTATCATTCATTTTAGGACAGGCAGTGTATCA
CACTGTGAAGCCAGCAGTTTTGCAGCAACAGTTAAAGAACATGCATCTTAGACAAGACATAGAAGAAGCATTGGTCAATG
CTTGGCCTACAATGGATGAAGAAGCAGTTGAAAAGTTCAGGCAAAGGATTTTGGCTCCCTACAAGCTAGAGATGGTTGAA
TGGCCACTTCATTTTCAAATGGATCACTCTGCTCAAGCAAAACTAAAACCTCCTCAAGCTGTGTTACAACCAGGAGTGAA
CAATGAAGATTCAAAGAGCCTGTAAAAAGTTCTTATGGAATTCAGTCCCAAGGAGTTGCTTGGTTTCTTTAACAAGCTAG
AGACCGCACAAGCACAGCTGGATTCCCTTACA

Alignment

ORF - retro_lafr_142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.81 %
• Parental protein coverage: 97.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALVLRETPSMKKAVSLINAIDTGRFPRLLTRILQKLHLKAESSFSEEEEEKLQAA-FSLEKQDLHLVLET
          AL..RETPSMKKAVSLINAIDTG.FP.LLT.ILQK.HLKAESSFSEEEEEKLQA..FSLEKQDLHLVLET
Retrocopy ALIVRETPSMKKAVSLINAIDTGTFPQLLTGILQKFHLKAESSFSEEEEEKLQAV>FSLEKQDLHLVLET

Parental  ISFILEQAVYHNVKPAALQQQLENIHLGQEKGEAFVNAWSAMGQEAVEKFRQRILAPHKLETVEWQLNLQ
          .SFIL.QAVYH.VKPA.LQQQL.N.HL.Q...EA.VNAW..M..EAVEKFRQRILAP.KLE.VEW.L..Q
Retrocopy VSFILGQAVYHTVKPAVLQQQLKNMHLRQDIEEALVNAWPTMDEEAVEKFRQRILAPYKLEMVEWPLHFQ

Parental  MAHSAQAKLKSPQAVLQLGVSNEDSKSLQKVLMEFSHKELFDFYNKLETIQAQLDSLT
          M.HSAQAKLK.PQAVLQ.GV.NEDSKSL.KVLMEFS.KEL..F.NKLET.QAQLDSLT
Retrocopy MDHSAQAKLKPPQAVLQPGVNNEDSKSL*KVLMEFSPKELLGFFNKLETAQAQLDSLT

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_142 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008311	2 retrocopies	retro_chof_1462, retro_chof_1585,
Cavia porcellus	ENSCPOG00000020474	1 retrocopy	retro_cpor_337,
Loxodonta africana	ENSLAFG00000011885	1 retrocopy	retro_lafr_142 ,
Microcebus murinus	ENSMICG00000006173	2 retrocopies	retro_mmur_1132, retro_mmur_607,
Myotis lucifugus	ENSMLUG00000010780	1 retrocopy	retro_mluc_2087,
Sarcophilus harrisii	ENSSHAG00000001698	1 retrocopy	retro_shar_261,
Tupaia belangeri	ENSTBEG00000004061	1 retrocopy	retro_tbel_3381,