RetrogeneDB ID: retro_lafr_963

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_52:4505910..4506181(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH
• Ensembl ID: ENSLAFG00000014841
• Aliases: None
• Description: None

Sequence

>retro_lafr_963
ATAGTGTTCCTGTTGGCAGCTTTCTGCTACATGTTGGTGCTGCTGGTGCTGCTCACTGCATCATGTAGCTTCTTCCCCAT
CTGGCACATTACAGCATTCAGAGAACCGAAGTCTAATTACAAGAATCCTATAGATGAGTGTATTACCCTGCATCCTCTTG
TATTTTCAAGAGCACTTCATCCATGATCTCCTCTGTGTAATGCTTCTTTGTGCAGTGGAGCAGCTTACACTGGGTCTCAA
TGCGTCACTCTTGGCACAGCATATTTGGAGG

Alignment

ORF - retro_lafr_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.74 %
• Parental protein coverage: 61.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAFTFAAFCYMLALL--LTATLIFFAIWHIIAFDELKTDYKNPIDQCNTLNPLV-LPEYLIHAFFCVMFL
          ..F..AAFCYML.LL..LTA...FF.IWHI.AF.E.K..YKNPID.C.TL.PLV...E..IH...CVM.L
Retrocopy IVFLLAAFCYMLVLLVLLTASCSFFPIWHITAFREPKSNYKNPIDECITLHPLV>FQEHFIHDLLCVMLL

Parental  CAAEWLTLGLNMPLLAYHIWR
          CA.E.LTLGLN..LLA.HIWR
Retrocopy CAVEQLTLGLNASLLAQHIWR

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_963 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031178	2 retrocopies	retro_cfam_658, retro_cfam_697,
Callithrix jacchus	ENSCJAG00000007306	1 retrocopy	retro_cjac_103,
Loxodonta africana	ENSLAFG00000014841	1 retrocopy	retro_lafr_963 ,
Nomascus leucogenys	ENSNLEG00000012704	1 retrocopy	retro_nleu_1896,
Otolemur garnettii	ENSOGAG00000024582	1 retrocopy	retro_ogar_2271,
Ochotona princeps	ENSOPRG00000005287	4 retrocopies	retro_opri_198, retro_opri_269, retro_opri_366, retro_opri_894,
Tupaia belangeri	ENSTBEG00000010265	3 retrocopies	retro_tbel_2080, retro_tbel_3728, retro_tbel_572,
Tarsius syrichta	ENSTSYG00000011295	1 retrocopy	retro_tsyr_1540,
Tursiops truncatus	ENSTTRG00000008259	1 retrocopy	retro_ttru_261,