RetrogeneDB ID: retro_lafr_637

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_27:18433976..18434375(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDKN3
• Ensembl ID: ENSLAFG00000014833
• Aliases: None
• Description: None

Sequence

>retro_lafr_637
TCATTGCAAACAAGTGAGTTTGACTCATCAGAAGAAGAGTCTATTAAAGGTGAACAGACTCCAATTCAGGTATCATGGCT
ATCCCTATCACAAGTGAATTGTTCTCTGTTTCTCAGTTTGTGTATTCTTCCAGGTTGTAAAATTAAAGATGTTAGAAGAA
ATATACAAAAAGATACCAAAGAACTAAAGAACTACGGTATACAAGACATATTTGTTTTCTGCACCAGAGGGGAGCTGTCA
AAATATACAGTCCCAAACCTTTTGGACCTCTACCAGCAGTATGGAATTATCACTCATCATCATCCAATCCCAGATGGCAG
GACTCCTGACATAGCCAGCTGCTGTGAAATAATGGAAGAGCTTGCAATCTGCCTTAAAAATAACCAAAAAACCGTAATA

Alignment

ORF - retro_lafr_637 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.47 %
• Parental protein coverage: 61.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLQTSEFDSSDEEPTEDEQTPIQISWLPLSRVNCSQFLGLCALPGCKFKDVRRNIQKDTEELKNYGIQDI
          SLQTSEFDSS.EE....EQTPIQ.SWL.LS.VNCS.FL.LC.LPGCK.KDVRRNIQKDT.ELKNYGIQDI
Retrocopy SLQTSEFDSSEEESIKGEQTPIQVSWLSLSQVNCSLFLSLCILPGCKIKDVRRNIQKDTKELKNYGIQDI

Parental  FVFCTRGELSKYRVPNLLDLYQQYGIITHHHPIPDGGTPDIASCCEIMEELAVCLKNNRKTLI
          FVFCTRGELSKY.VPNLLDLYQQYGIITHHHPIPDG.TPDIASCCEIMEELA.CLKNN.KT.I
Retrocopy FVFCTRGELSKYTVPNLLDLYQQYGIITHHHPIPDGRTPDIASCCEIMEELAICLKNNQKTVI

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_637 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012823	1 retrocopy	retro_chof_1806,
Echinops telfairi	ENSETEG00000018617	1 retrocopy	retro_etel_1763,
Felis catus	ENSFCAG00000015089	2 retrocopies	retro_fcat_135, retro_fcat_626,
Loxodonta africana	ENSLAFG00000014833	1 retrocopy	retro_lafr_637 ,
Macropus eugenii	ENSMEUG00000002497	3 retrocopies	retro_meug_1255, retro_meug_1768, retro_meug_1849,
Procavia capensis	ENSPCAG00000015559	1 retrocopy	retro_pcap_104,
Sarcophilus harrisii	ENSSHAG00000008977	1 retrocopy	retro_shar_502,
Tupaia belangeri	ENSTBEG00000010203	2 retrocopies	retro_tbel_1809, retro_tbel_4700,