RetrogeneDB ID: retro_lafr_994

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_58:13134746..13135264(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN6
• Ensembl ID: ENSLAFG00000027296
• Aliases: None
• Description: None

Sequence

>retro_lafr_994
AAGAGCGCCCTCTTGATCTACACTTCCATCTTCTGGATCACTGGTGTTATCGTTCTTGCCATTTGCACTGGGGCAAGGTG
AGCCTGGAGAATTATTTTTCACTTTTAAATAAGAAGGCCACCAATGTCCCCTTCATATTCCTTGGCACTGGCACTGTCAT
TATTCTTTTGGGCACCTTTGGCTATTTTGCTACTTGCTGAGCTTCTGCATGGATGCTAAAACTATATGCAGTATTTATGA
CTCTCATTTTTTTGGTCGAACTGGTCGCTGCCGTCATAGGATTTGTTTTCTGACATGAGATAAAGAACAGCTTTAAGAAT
AATTATGAGAAAGGTCTGAAGCAATATAACATGACAGGAGATTATAGAAGCAATGCTATATACAAGATCCAGAATAAAAT
GCATTGTTGTGGTGTCACCAAATACACAGATTGGGAAGATACTAATTATTACTCAGAACAAAGCTATCCCAAGCACTGCT
CTAAAACTGAATGTTCTCCAAGCAAAGATGCAAGTAAA

Alignment

ORF - retro_lafr_994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.03 %
• Parental protein coverage: 70.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSILLIYTFIFWITGVILLAVGI-WGKVSLENYFSLLNEKATNVPFILVGTGTGIILWGTFGCFATCRVS
          KS.LLIYT.IFWITGVI.LA....WGKVSLENYFSLLN.KATNVPFI..GTGT.IIL.GTFG.FATC..S
Retrocopy KSALLIYTSIFWITGVIVLAICT<WGKVSLENYFSLLNKKATNVPFIFLGTGTVIILLGTFGYFATC*AS

Parental  AWMLKLYAMVLTLIFLVELVAAIVGFVFRHEIKNSFKNNYEKALKQYNMTGDDRSDAVDKIQNTLHCCGV
          AWMLKLYA...TLIFLVELVAA..GFVF.HEIKNSFKNNYEK.LKQYNMTGD.RS.A..KIQN..HCCGV
Retrocopy AWMLKLYAVFMTLIFLVELVAAVIGFVF*HEIKNSFKNNYEKGLKQYNMTGDYRSNAIYKIQNKMHCCGV

Parental  TKYTDWENTNYYSERGYPKSCCKTECSPSKDASK
          TKYTDWE.TNYYSE..YPK.C.KTECSPSKDASK
Retrocopy TKYTDWEDTNYYSEQSYPKHCSKTECSPSKDASK

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_994 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017521	3 retrocopies	retro_cfam_1600, retro_cfam_1609, retro_cfam_878,
Callithrix jacchus	ENSCJAG00000004288	1 retrocopy	retro_cjac_2306,
Echinops telfairi	ENSETEG00000012276	1 retrocopy	retro_etel_1987,
Loxodonta africana	ENSLAFG00000027296	1 retrocopy	retro_lafr_994 ,
Microcebus murinus	ENSMICG00000011370	1 retrocopy	retro_mmur_447,
Nomascus leucogenys	ENSNLEG00000007505	1 retrocopy	retro_nleu_1186,
Otolemur garnettii	ENSOGAG00000004869	1 retrocopy	retro_ogar_2827,
Sarcophilus harrisii	ENSSHAG00000000274	1 retrocopy	retro_shar_515,
Sus scrofa	ENSSSCG00000012481	1 retrocopy	retro_sscr_84,