RetrogeneDB ID: retro_lafr_222

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:110368109..110368509(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTC
• Ensembl ID: ENSLAFG00000026381
• Aliases: None
• Description: oligosaccharyltransferase complex subunit (non-catalytic) [Source:HGNC Symbol;Acc:24448]

Sequence

>retro_lafr_222
TGCCCCAGTCTGAAACTGAAGAAGCTGACCTGGGTGCACATACAGTGTCCATGATGGTGTACGCTCTGGTAGTGGTGTCT
TACTTCCTTATCACTGGAGGAATAATTTATAACGTTATTGTGGAACCTCCAAATGTTGACGTTATGACTGATGAACATGG
GCATCAAAGACCAGTAGCTTTCTTGACTACAGAGTAAATGGACAATACATTATGGAAGGACTTGCTTCCTGTTTACAATA
GGGAAGGGGGTTAGGTTTCATAATTCTGGACCCATCCAGTGCACCAAATATCCCAAAACTCAATAGATTTCTTCTATTTA
TTGAATTTGTCTGTGCCCTATTGAACTTTTTTAGGGCTAGGATATTCATGAGAATGAAACTGCTGACCTATCTGATGGGT

Alignment

ORF - retro_lafr_222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.36 %
• Parental protein coverage: 91.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CPNLKLKKPPWVHMPS-AMTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQRPVAFLA-YRVNG
          CP.LKLKK..WVH.....M.VYALVVVSYFLITGGIIY.VIVEPP.V..MTDEHGHQRPVAFL..YRVNG
Retrocopy CPSLKLKKLTWVHIQC<SMMVYALVVVSYFLITGGIIYNVIVEPPNVDVMTDEHGHQRPVAFLT<YRVNG

Parental  QYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLLSFFMARVFMRMKLPFFLLG
          QYIMEGLAS......G.LGFIILD.S.APNIPKLNRF.LLFI.FVC.LL.FF.AR.FMRMKL...L.G
Retrocopy QYIMEGLASCLQ*GRG-LGFIILDPSSAPNIPKLNRF-LLFIEFVCALLNFFRARIFMRMKLLTYLMG

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_222 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 13 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011611	1 retrocopy	retro_btau_753,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Dasypus novemcinctus	ENSDNOG00000011172	2 retrocopies	retro_dnov_12, retro_dnov_1973,
Homo sapiens	ENSG00000198856	7 retrocopies	retro_hsap_1746, retro_hsap_2013, retro_hsap_2972, retro_hsap_3598, retro_hsap_3686, retro_hsap_376, retro_hsap_4246,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Loxodonta africana	ENSLAFG00000026381	7 retrocopies	retro_lafr_1046, retro_lafr_17, retro_lafr_222 , retro_lafr_231, retro_lafr_444, retro_lafr_549, retro_lafr_618,
Myotis lucifugus	ENSMLUG00000000478	2 retrocopies	retro_mluc_1366, retro_mluc_1511,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Nomascus leucogenys	ENSNLEG00000012929	11 retrocopies	retro_nleu_1372, retro_nleu_1436, retro_nleu_2026, retro_nleu_2265, retro_nleu_2274, retro_nleu_2665, retro_nleu_2796, retro_nleu_2826, retro_nleu_297, retro_nleu_474, retro_nleu_923,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Otolemur garnettii	ENSOGAG00000033684	1 retrocopy	retro_ogar_578,
Pan troglodytes	ENSPTRG00000024222	1 retrocopy	retro_ptro_34,
Tursiops truncatus	ENSTTRG00000003446	1 retrocopy	retro_ttru_582,