RetrogeneDB ID: retro_lafr_101

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_68:3707993..3709049(+)
• Located in intron of: ENSLAFG00000031153

Retrocopy information

• Ensembl ID: ENSLAFG00000031477
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GPD1L
• Ensembl ID: ENSLAFG00000013996
• Aliases: None
• Description: None

Sequence

>retro_lafr_101
ATGGCAGCAACACCCCTCAAAGTGTGCATCCTGGGCTCGGGGAACTGGGGTTCAGCTGTTGCAAAAATAATTGGTAATAA
TGTCAAGAAACTTCAGAAGTTTGCCTCCACGGTCAAGATGTGGGTCTTTGAAGAAACGGTTAATGGGAGAAAACTGACAG
ACATCATAAACAACGACCATGAAAATGTAAAATATCTCCCTGGACACAAGCTGCCAGACAATGTGGTTGCAGTTTCAAAT
CTCAACGAGGCCGTGCAGGACGCAGACCTGCTGGTGTTTGTCATTCCTCACCAGTTCATTCATAGAATCTGTGATGAGAT
CACTGGGAGGGTGCCCAAGAAAACACTAGGAATCAGCCTCATCAAGGGGATAGATGAGGGCCCTGAGGGGCTGAAACTCA
TTTCCGACATCATTCGAGAGAAGGTGGGCATTGACATCAGTGTGCTCATGGGAGCCAATACTGCCAACGATGTGGCCGCA
GATGAGTTCTGTGAGACCACCATTGGCAGCAAAGAAATGAAGAATGGCCTTCTCTTCAAAGAACTTCTGCAGACTCCAAA
TTTCCTGATTACAGTGGTTGATGATGCAGATACTGTTGAACTTTGCGGTGCTCTTAAGAACATCGTAGCTGTGGGAGCCG
GGCTCTGTGATGGTCTGCGCTACGGAGACAACACCAAAGCTGCAGTCATCCGCCTCGGACTCGTGGAGATGATCTCATTT
GCCAGGATCTTCTGCAAGGGCCAGGTGTCCACAGCCACCTTCCTAGAGAGCTGTGGGGTGGCTGACCTGATCACCACCTG
CTATGGAGGCCGGAACCGCAAGGTGGCTGAGGCGTTTGTCAGGACTGGAAAGACCATTGAAGAATTAGAGAGAGAGATGC
TGGATGGGCAGAAACTCCAAGGACCTCAGACTTCTGCTGAAGTGTACCGCATCCTCAAGAAGAAGGGACTAATCGACAAG
TTTCCGTTGTTCACTGCTGTATATCAGATTTGCTATGAAGGAAAACCCGTTCAAGATCTGTTGTCTTGTCTCCAGTACCA
TCCAGTGCGCACATAA

Alignment

ORF - retro_lafr_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAPLKVCIVGSGNWGSAVAKIIGNNVKKLQKFASTVKMWVFEETVNGRKLTDIINNDHENIKYLPGHK
          MAA.PLKVCI.GSGNWGSAVAKIIGNNVKKLQKFASTVKMWVFEETVNGRKLTDIINNDHEN.KYLPGHK
Retrocopy MAATPLKVCILGSGNWGSAVAKIIGNNVKKLQKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHK

Parental  LPENVVAVSNLKEAVQDADLLVFVIPHQFIHRICDEITGRVSKGALGITLIKGIDKGPDGLKLISDIIRE
          LP.NVVAVSNL.EAVQDADLLVFVIPHQFIHRICDEITGRV.K..LGI.LIKGID.GP.GLKLISDIIRE
Retrocopy LPDNVVAVSNLNEAVQDADLLVFVIPHQFIHRICDEITGRVPKKTLGISLIKGIDEGPEGLKLISDIIRE

Parental  KVSIDISVLMGANIANEVAAEKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNIVA
          KV.IDISVLMGAN.AN.VAA..FCETTIGSK.M.NGLLFKELLQTPNF.ITVVDDADTVELCGALKNIVA
Retrocopy KVGIDISVLMGANTANDVAADEFCETTIGSKEMKNGLLFKELLQTPNFLITVVDDADTVELCGALKNIVA

Parental  VGAGFCDGLHCGDNTKAAVIRLGLMEMISFARIFCRGHVSTATFLESCGVADLITTCYGGRNRRVAEAFA
          VGAG.CDGL..GDNTKAAVIRLGL.EMISFARIFC.G.VSTATFLESCGVADLITTCYGGRNR.VAEAF.
Retrocopy VGAGLCDGLRYGDNTKAAVIRLGLVEMISFARIFCKGQVSTATFLESCGVADLITTCYGGRNRKVAEAFV

Parental  RTGKTIEELEKEMLNGQKLQGPQTSAEVYRILKQKGLIDKFPLFTAVYQICYEGKPVKDMLSCLQCHPEH
          RTGKTIEELE.EML.GQKLQGPQTSAEVYRILK.KGLIDKFPLFTAVYQICYEGKPV.D.LSCLQ.HP..
Retrocopy RTGKTIEELEREMLDGQKLQGPQTSAEVYRILKKKGLIDKFPLFTAVYQICYEGKPVQDLLSCLQYHPVR

Parental  T
          T
Retrocopy T

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_101 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009826	1 retrocopy	retro_btau_1671,
Choloepus hoffmanni	ENSCHOG00000012633	5 retrocopies	retro_chof_1033, retro_chof_306, retro_chof_340, retro_chof_620, retro_chof_724,
Loxodonta africana	ENSLAFG00000013996	1 retrocopy	retro_lafr_101 ,
Microcebus murinus	ENSMICG00000011060	1 retrocopy	retro_mmur_1205,
Mus musculus	ENSMUSG00000050627	3 retrocopies	retro_mmus_1348, retro_mmus_2552, retro_mmus_3695,
Oryctolagus cuniculus	ENSOCUG00000010093	2 retrocopies	retro_ocun_1529, retro_ocun_1588,
Otolemur garnettii	ENSOGAG00000013243	1 retrocopy	retro_ogar_285,
Procavia capensis	ENSPCAG00000016132	1 retrocopy	retro_pcap_316,
Rattus norvegicus	ENSRNOG00000026455	2 retrocopies	retro_rnor_2035, retro_rnor_2474,
Sus scrofa	ENSSSCG00000021977	1 retrocopy	retro_sscr_154,