RetrogeneDB ID: retro_lafr_818

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:77088507..77088927(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC1
• Ensembl ID: ENSLAFG00000012844
• Aliases: None
• Description: None

Sequence

>retro_lafr_818
AGAGCTACAGGTAAAACATGCCTATTGACCAGCTACACGATTGATGCATTTCCTAGAGAATATATCCCCACGGTCTTTGA
AAACTATTCTGCCAATGTTATGGTAAACGGAAAAGCAGTGAATCTGGGTTTATGGGATACAGATGGACAAAAAGATTATG
ACAGATTGCACCCACTATCCTATCTGCAAACAGATGTATTCTTAATCTGCTTTGCCCTGCGAGTGCTTCACCATTTGAAA
ATGTCCACGCAAAGTAGCATCCTGAAGTGCAACACCATTGTGTGAACACTCCTACAATCCTACTGGGAACCAACCCTGAT
CTGAGAGATGAAAAGACACAATTTGAAACTGAAGGAGAAGCAGCTGGCTCCTATCACCTATCCAACACGGTTTAGCTCTG
ACTGTGAAATACATGGAATT

Alignment

ORF - retro_lafr_818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.44 %
• Parental protein coverage: 73.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLNC
          RA.GKTCLL.SYT..AFP.EYIPTVF.NYSANVMV.GK.VNLGLWDT.GQ.DYDRL.PLSY.QTDVFL.C
Retrocopy RATGKTCLLTSYTIDAFPREYIPTVFENYSANVMVNGKAVNLGLWDTDGQKDYDRLHPLSYLQTDVFLIC

Parental  FSL-VSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDD-KDTI-EKLKEKKLTPITYPQGLAMAKE
          F.L..S...FENV.AK..PEV.HHC.NTP.IL.GT..DLRD..KDTI..KLKEK.L.PITYP.......E
Retrocopy FAL<ASASPFENVHAK*HPEVQHHCVNTPTILLGTNPDLRDE<KDTI<LKLKEKQLAPITYPTRFSSDCE

Parental  IGAV
          I...
Retrocopy IHGI

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_818 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 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000011361	2 retrocopies	retro_fcat_1632, retro_fcat_717,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Loxodonta africana	ENSLAFG00000012844	1 retrocopy	retro_lafr_818 ,
Loxodonta africana	ENSLAFG00000013012	1 retrocopy	retro_lafr_117,
Myotis lucifugus	ENSMLUG00000009701	1 retrocopy	retro_mluc_1059,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,