RetrogeneDB ID: retro_lafr_1088

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_68:1301402..1302016(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN13
• Ensembl ID: ENSLAFG00000005956
• Aliases: None
• Description: None

Sequence

>retro_lafr_1088
ATGGTTTGCAGGGGACTTCGCATGTCCTAAGAACTGCCTGTGCTCCCTCAACCCGCTCTACATCTTGGTCAGCCTGCTGC
TAATTGGAATTGCTGTGTGAGGCATTGGCTTTGGGCTGATTTCCAGTCTCCGGGCGGTCAGTGTGGTCATTGCAGTGGGC
GCCCTTCCGTTCCTGATTGCATTAGTGGGCTTATTAGAGCCAAATAACACCATAAGATTTCTTTCTTTTTTTTTTTTTTA
CATGATTATTCTCTTACTTGTATTTATTGTTCAGTGTTCTGTATCCTGGGCTTATTTAGCCCTGAACCAGGAGCAACAGG
GTTAGCTTCTGGAAATTGGTTGGAACAATACAACAAGTGCTTGAAATGACATCCAGAGAAATTTAAACTGCTGTGGTTTC
TGAAGTTTTAGCCCAATGACACCTGTTTGGCTACCTGTCTCAAAAGCCGTCACCAGTGCTCGCCGTGTGTTCCGATAATA
GGAGAATATGCCAGAGAGGTTTTGAGATTTCTTGGCAGCATTGGCCTGTTCTGTTTTACAGAGATCCTGGGCGTTTGGCT
GACCTAGAGTTACAGGAACCAGAAAGATCCTCGAGTAATCCTAGTGCGTTCCTG

Alignment

ORF - retro_lafr_1088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVC-GGFACSKNCLCALNLVYTLVSLLLIGIAAWGIGFGLISSLRVVGVVIAVGIFLFLIALVGLIGAVK
          MVC.G.FAC.KNCLC.LN..Y.LVSLLLIGIA..GIGFGLISSLR.V.VVIAVG...FLIALVGL.....
Retrocopy MVC>GDFACPKNCLCSLNPLYILVSLLLIGIAV*GIGFGLISSLRAVSVVIAVGALPFLIALVGLLEPNN

Parental  HHQVLLFFYMIILLL--VFIFQFSVSCACLALNQDQQGQLLEVGWNNTASARNDIQRNLNCCGFRSVN-P
          ....L.FF......L..VFI.Q.SVS.A.LALNQ.QQG.LLE.GWNNT.SA.NDIQRNLNCCGF.S...P
Retrocopy TIRFLSFFFFYMIILLLVFIVQCSVSWAYLALNQEQQG*LLEIGWNNTTSA*NDIQRNLNCCGF*SFS<P

Parental  NETCLASCVKSGHQCSPCAPIIEEYAGEVLRFVGGIGLFFSFTEILGVWLTYRYRNQKDPR-ANPSAFL
          N.TCLA.C.KS.HQCSPC.PII.EYA.EVLRF.G.IGL.F.FTEILGVWLT..YRNQKDPR..NPSAFL
Retrocopy NDTCLATCLKSRHQCSPCVPIIGEYAREVLRFLGSIGL-FCFTEILGVWLT*SYRNQKDPR<SNPSAFL

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_1088 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010524	1 retrocopy	retro_amel_1425,
Loxodonta africana	ENSLAFG00000005956	3 retrocopies	retro_lafr_1088 , retro_lafr_195, retro_lafr_556,
Ictidomys tridecemlineatus	ENSSTOG00000008833	1 retrocopy	retro_itri_1367,
Tursiops truncatus	ENSTTRG00000009870	1 retrocopy	retro_ttru_551,