RetrogeneDB ID: retro_lafr_1169

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:29278333..29278999(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM3C
• Ensembl ID: ENSLAFG00000010029
• Aliases: None
• Description: None

Sequence

>retro_lafr_1169
GGTGCCGCAAAGTTGGTGGTAGCTGTGGCAGCATATTTACTGACATTTTATGTAATATCTCAAGTATTTGAAAACAAATG
GATGCAAGTTTAGGAAACATATTTGCAAGGTCAGCATTGAACACAGCTACCCGTTCTACTAAGCCTCCAAGATGTGAATG
TGGCATCTCAAAATCTTGCCCTGAGAAGCATTTTGCTTCTAAAATGGCAAGTGGATCAGCCAACATGTTGGGCCCAAAAA
TTTGTTTGGAAGACAATGTTTTCATGAGTGGTGTTAAGAATAACATTGGAAGAGCAATCAGTGCTGCCTTGGTAGATGGA
AAAGGAGGAGAAGTATTAGACAGTAAATATTTTGACATGTGTGGAGAGGAGCAGCACCATTTATTAAGTTTCAAAGTCTA
TACAAGATGGAACAGTAGTCATAATTGGAACATACGATGATGGAGCAACCAAACTCAACAACGAGGTATAGCGGCTCATT
GCTGAATTGGGGAGTACATCTTTTACTAATTTTGGATTTAGAGATAGCTGGGTCTTCTGTGGTGGGAAACACATTAAGAT
AAAAAGCCCTTTTGAACAGCACATAAAGAACAATAAGGATATGAACAAATACGAAGGATGGCCGGAAGTCGTAGAAATGG
ACAGAAGCATCACCCGGAAGCAAGAC

Alignment

ORF - retro_lafr_1169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.99 %
• Parental protein coverage: 98.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GVAKLVVAVAVFLLTFYVISQVFEIK-MDASLGNLFARSALDTAARSTKPPKYKCGISKACPEKHFAFKM
          G.AKLVVAVA..LLTFYVISQVFE.K.MDASLGN.FARSAL.TA.RSTKPP...CGISK.CPEKHFA.KM
Retrocopy GAAKLVVAVAAYLLTFYVISQVFENK<MDASLGNIFARSALNTATRSTKPPRCECGISKSCPEKHFASKM

Parental  ASGAANVVGPKICLEDNILMSGVKNNVGRGINVALVNGKTGELLNTKYFDMWGGD-VAPFIEF-LKSIQD
          ASG.AN..GPKICLEDN..MSGVKNN.GR.I..ALV.GK.GE.L..KYFDM.G....APFI.F..KSIQD
Retrocopy ASGSANMLGPKICLEDNVFMSGVKNNIGRAISAALVDGKGGEVLDSKYFDMCGEE<AAPFIKF<SKSIQD

Parental  GTIVLMGTYDDGATKLNDEARRLIAELGSTSITNLGFRDNWVFCGGKGIKTKSPFEQHIKNNKDTNKYEG
          GT.V..GTYDDGATKLN.E..RLIAELGSTS.TN.GFRD.WVFCGGK.IK.KSPFEQHIKNNKD.NKYEG
Retrocopy GTVVIIGTYDDGATKLNNEV*RLIAELGSTSFTNFGFRDSWVFCGGKHIKIKSPFEQHIKNNKDMNKYEG

Parental  WPEVVEMEGCIPQKQD
          WPEVVEM...I..KQD
Retrocopy WPEVVEMDRSITRKQD

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_1169 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003224	1 retrocopy	retro_chof_1467,
Felis catus	ENSFCAG00000023087	1 retrocopy	retro_fcat_1392,
Homo sapiens	ENSG00000196937	1 retrocopy	retro_hsap_4657,
Loxodonta africana	ENSLAFG00000010029	1 retrocopy	retro_lafr_1169 ,
Macropus eugenii	ENSMEUG00000006906	2 retrocopies	retro_meug_2057, retro_meug_536,
Monodelphis domestica	ENSMODG00000015478	1 retrocopy	retro_mdom_1392,
Sarcophilus harrisii	ENSSHAG00000015103	1 retrocopy	retro_shar_6,
Tursiops truncatus	ENSTTRG00000016229	2 retrocopies	retro_ttru_1219, retro_ttru_855,