RetrogeneDB ID: retro_lafr_195

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:104058050..104058602(+)
• Located in intron of: ENSLAFG00000029002

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_195
ACCTTGGTTAGCCTGCTGCTGCTAATTGGAATTGCTGTGCAGGGCGTTGACTTCTGGCTGATTTCTAGCGTCAGGGTGGT
CGGTGCGGTCATTGCAGTGGGCATCTTTCTTGTTCCTCATTGCATTAGCGGAGCTGATTGGAGCTGTAAAACGCCCTCAG
GTGTTGCGATTTTTTACGATTGTCCTCCTACTTGTATTTATTGTTCAGTTTTTTTGTGTGTGCTTGCTTAGCCCTGAGCC
AGGATCAACAGGATTAGCTTCTGGAAGTTGACTGGAGTAATACAGTAAGTACCTGAAATGGCATCCAGAGAAATTTTGAC
TACTGTGGGTTCTGAAGTTTTAATCCAAAGGACACCCGTTTGGCTAGCTGTGTTAAAAGTGGCCAGCAGTGCTCACAGCA
TGCTTTGATAATAGGAGAATATGCCGGAGAGGTTTTGAGATTTGAGAACAGGCACTGGCCTCTTCTTCAGTTTTACAGAG
CTCTTGGGCATTTGCCTGACCGACAGGCACAGGAACCAGAAAGATCCTGGTGCTAATTCTAGTGTATTCCTT

Alignment

ORF - retro_lafr_195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.74 %
• Parental protein coverage: 90.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TLVSLLL-IGIAAWGIGFGLISSLRVVGVVIAVGIFL-FLIALVGLIGAVKHHQVLLFFYMIILLLVFI-
          TLVSLLL.IGIA..G..F.LISS.RVVG.VIAVGIFL.FLIAL..LIGAVK..QVL.FF..I.LLLVFI.
Retrocopy TLVSLLLLIGIAVQGVDFWLISSVRVVGAVIAVGIFL>FLIALAELIGAVKRPQVLRFF-TIVLLLVFI>

Parental  FQFSVSCACLALNQDQQGQLLEVGWNNTASARNDIQRNLNCCGFRSVNPNETCLASCVKSGHQCSPCAPI
          F.F.V.CACLAL.QDQQ..LLEV.W.NT.S..N.IQRN...CGF.S.NP..T.LASCVKSG.QCS..A.I
Retrocopy FSFFV-CACLALSQDQQD*LLEVDWSNTVST*NGIQRNFDYCGF*SFNPKDTRLASCVKSGQQCSQHALI

Parental  IEEYAGEVLRFVG-GIGLFFSFTEILGVWLTYRYRNQKDPRANPSAFL
          I.EYAGEVLRF...G.GLFFSFTE.LG..LT.R.RNQKDP.AN.S.FL
Retrocopy IGEYAGEVLRFEN>GTGLFFSFTELLGICLTDRHRNQKDPGANSSVFL

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_195 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,