RetrogeneDB ID: retro_lafr_65

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_104:1728767..1729526(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000003671
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PSMB8
• Ensembl ID: ENSLAFG00000003213
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:G3SRY0]

Sequence

>retro_lafr_65
ATGGCTCTGCAGGATGTGTGCAACTGGCAGGCCCTTGATACCCAAGGACTATCACCTCACCTGCCTCAGGCTGGTGGCTG
GGCCATGCCACCGGGCTGCGATCCTCAAACCTTCCTGCAGATCCATGGCCCCAAGCTGGCCCATGGCACCACCACCCTGG
CCTTCCGTTTCTGTCATGGAGTCATTGCTGCAGCTGACACGCGCTCTTCCTGTAACAACTACATGGCTTGTCCAGCCTCA
CGCAAAGTCATTCCTGTGCACCAGCACCTCCTGGGCACCACCTCTGGCACCTCTGCCGACTGCGTCACTTGGTACCGGGT
GCTACAGCGGGAGCTGCGGCTGCGGGCACTGAGGGAGGGTCAACTGCCCAGTGTGGCTAGCGCTGCCAAACTCTTGTCAG
CCATGATGTCCCGCTACCGTGGGCTGGATCTATGTGTGGCCACTGCCCTGTGTGGTTGGGACCGCTCAGGCCCTGCCCTC
TTCTACGTCTACAGCGACGGCACTCGCCTGCAGGGGGACATCTTCTCGGTGGGCTCTGGATCTCCATATGCCTATGGTGT
GCTAGACCGAGGCTACCGCTATGACATGACCACCCAGGAAGCCTACACTCTGGCTCGCTGTGCAGTGGCCCATGCCACCC
GCCGTGATGCCTATTCTGGGGGTTCTGTGGACCTTTTCCACGTGCGGGAGAGTGGATGGGAGTACGTGTCTCGTGAGGAT
GCCTGTGTGCTGTACACGGAGCTGCAAGAGCCCTCGAAG

Alignment

ORF - retro_lafr_65 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.2 %
• Parental protein coverage: 75.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EMNHGTTTLAFKFQHGVIVAVDSRASAGTYIANLQTKKVIEINPYLLGTMSGSAADCQYWERLLAKECRL
          ...HGTTTLAF.F.HGVI.A.D.R.S...Y.A.....KVI.....LLGT.SG..ADC..W.R.L..E.RL
Retrocopy KLAHGTTTLAFRFCHGVIAAADTRSSCNNYMACPASRKVIPVHQHLLGTTSGTSADCVTWYRVLQRELRL

Parental  YYLRNGERISVSAASKLLSNMMCQYRGMGLSMGSMICGWDKKGPGLYYVDDSGTRLSGSMFSTGSGNPYA
          ..LR.G...SV..A.KLLS.MM..YRG..L......CGWD..GP.L.YV...GTRL.G..FS.GSG.PYA
Retrocopy RALREGQLPSVASAAKLLSAMMSRYRGLDLCVATALCGWDRSGPALFYVYSDGTRLQGDIFSVGSGSPYA

Parental  YGVMDSGYQPNLSPEEAYDLARRAIAHATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYRETNQ
          YGV.D.GY.......EAY.LAR.A.AHAT.RD.YSGG.V...H..E.GW..V...D...L.....E...
Retrocopy YGVLDRGYRYDMTTQEAYTLARCAVAHATRRDAYSGGSVDLFHVRESGWEYVSREDACVLYTELQEPSK

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_65 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002026	1 retrocopy	retro_amel_27,
Bos taurus	ENSBTAG00000003039	1 retrocopy	retro_btau_11,
Canis familiaris	ENSCAFG00000000829	1 retrocopy	retro_cfam_75,
Equus caballus	ENSECAG00000018887	1 retrocopy	retro_ecab_18,
Felis catus	ENSFCAG00000023131	1 retrocopy	retro_fcat_30,
Loxodonta africana	ENSLAFG00000003213	1 retrocopy	retro_lafr_65 ,
Microcebus murinus	ENSMICG00000015254	1 retrocopy	retro_mmur_33,
Myotis lucifugus	ENSMLUG00000013876	1 retrocopy	retro_mluc_285,
Monodelphis domestica	ENSMODG00000014366	1 retrocopy	retro_mdom_179,
Otolemur garnettii	ENSOGAG00000013830	1 retrocopy	retro_ogar_256,
Procavia capensis	ENSPCAG00000016741	1 retrocopy	retro_pcap_21,
Pan troglodytes	ENSPTRG00000018022	2 retrocopies	retro_ptro_1102, retro_ptro_97,
Pteropus vampyrus	ENSPVAG00000002800	1 retrocopy	retro_pvam_20,
Sus scrofa	ENSSSCG00000026951	1 retrocopy	retro_sscr_90,
Tupaia belangeri	ENSTBEG00000007794	1 retrocopy	retro_tbel_2055,
Tarsius syrichta	ENSTSYG00000007730	1 retrocopy	retro_tsyr_1639,