RetrogeneDB ID: retro_lafr_427

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_16:24975443..24975898(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLP2
• Ensembl ID: ENSLAFG00000004483
• Aliases: None
• Description: None

Sequence

>retro_lafr_427
CTGGAGGATTCCGAGTTCCTCTCAGCCCCCAGCTTGCTGAGCCCTTTGCACCAACTTCTCTTGCACCAGAAAGGGAACTC
CCCTGTCTGCTGAGATTATATTGAGCCAGGTTGTTCTGATCTGTTTCAGTGGTTCGGCACAGTATCGAGGGTACTCCTGC
CTATTGGTGGCTGAGATAGTGCTTGCTGCTTTCTTATTTGTCATCTATATGTTGTAACTTGCACACTAAGATTCAGTTCA
CCAACTGGCCCTAGTGCGATTCCTTCCAAACCCTCAAAGCCGAGATGCTGCTCATGCCCATTGTTGTCCTTGTTGAGGAA
GAAAACAACTGAAATATCTTCACCAGGGTACTGGGCCTAATCACAGTGAACTTTTCTGGATATAATGCTTGCATCACCTT
TCCCTTGCAGCAACAAAGCCACACAGCAGAACCCACTGACCCCATAGATGGACCT

Alignment

ORF - retro_lafr_427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADSERLSAPG-CWIACTNFSRTRKGILLFAEIILCLVILICFSAPANGQAYYSSLPVFEMILAAVFFVI
          ..DSE.LSAP..C...CTNFS.TRKG..L.AEIIL..V.LICFS..A.....YS.L.V.E..LAA..FVI
Retrocopy LEDSEFLSAPS>C*ALCTNFSCTRKGTPLSAEIILSQVVLICFSGSAQYRG-YSCLLVAEIVLAAFLFVI

Parental  YM-CDLHTKIQFINWPWSDFFRALIAAILFLITSIIVLVEKGKASKIIAGVLGLISTCLFGYDAYITFPF
          YM.C.LHTKIQF.NWP..D.F..L.A..L.....I.VLVE......I...VLGLI.....GY.A.ITFP.
Retrocopy YM>CNLHTKIQFTNWP*CDSFQTLKAEMLLM--PIVVLVEEENN*NIFTRVLGLITVNFSGYNACITFPL

Parental  RQQRHTAAPTDPADGP
          .QQ.HTA.PTDP.DGP
Retrocopy QQQSHTAEPTDPIDGP

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_427 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 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012288	1 retrocopy	retro_amel_1129,
Bos taurus	ENSBTAG00000016093	3 retrocopies	retro_btau_1574, retro_btau_73, retro_btau_810,
Canis familiaris	ENSCAFG00000015798	1 retrocopy	retro_cfam_933,
Equus caballus	ENSECAG00000000216	1 retrocopy	retro_ecab_971,
Felis catus	ENSFCAG00000003820	2 retrocopies	retro_fcat_1547, retro_fcat_256,
Homo sapiens	ENSG00000102007	1 retrocopy	retro_hsap_3411,
Loxodonta africana	ENSLAFG00000004483	1 retrocopy	retro_lafr_427 ,
Macaca mulatta	ENSMMUG00000023022	1 retrocopy	retro_mmul_2124,
Mustela putorius furo	ENSMPUG00000013817	3 retrocopies	retro_mputfur_107, retro_mputfur_462, retro_mputfur_969,
Mus musculus	ENSMUSG00000031146	1 retrocopy	retro_mmus_94,
Nomascus leucogenys	ENSNLEG00000001317	1 retrocopy	retro_nleu_2887,
Otolemur garnettii	ENSOGAG00000003865	3 retrocopies	retro_ogar_2568, retro_ogar_2865, retro_ogar_473,
Pan troglodytes	ENSPTRG00000021885	1 retrocopy	retro_ptro_2316,
Pteropus vampyrus	ENSPVAG00000011770	2 retrocopies	retro_pvam_1214, retro_pvam_810,
Rattus norvegicus	ENSRNOG00000039496	1 retrocopy	retro_rnor_2686,
Tursiops truncatus	ENSTTRG00000016968	2 retrocopies	retro_ttru_1586, retro_ttru_767,