RetrogeneDB ID: retro_lcha_65

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127152.1:321561..321772(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: eif1axb
• Ensembl ID: ENSLACG00000015565
• Aliases: None
• Description: eukaryotic translation initiation factor 1A, X-linked, b [Source:ZFIN;Acc:ZDB-GENE-030131-1319]

Sequence

>retro_lcha_65
AAGGTCTGGACGAACACTTCAGACATGAGACTGGTTGGACTACGAGATAACCAGGACATCTAGACTGAGCTCATTCGAAA
ATATAATGTAGATGAAGCCAGAAGCTTGAAAGCGTATGGTGAACTTCACAACATGCCAAAAATCAAATCAGACAGACACA
TTTGGTCCTGGTTATGATGATGAGACCTAGTTTGATGATACCGGAGATGAC

Alignment

ORF - retro_lcha_65 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.61 %
• Parental protein coverage: 85.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVWINTSDIILIGLRDYQDTKADVILKYNADEARSLKAYGELPEHAKI-NETDTFGPGDDDEIQFDDIGD
          .VW.NTSD..L.GLRD.QD.....I.KYN.DEARSLKAYGEL....KI.N.TDTFGPG.DDE..FDD.GD
Retrocopy KVWTNTSDMRLVGLRDNQDI*TELIRKYNVDEARSLKAYGELHNMPKI>NQTDTFGPGYDDET*FDDTGD

Parental  D
          D
Retrocopy D

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
DRP000627_gill	0.06 RPM	70.75 RPM
DRP000627_kidney	0.08 RPM	68.04 RPM
DRP000627_pectoral_fin	0.04 RPM	60.01 RPM
DRP000627_pelvic_fin	0.00 RPM	82.04 RPM
DRP000627_pharynx	0.18 RPM	88.32 RPM
DRP000627_tail_muscle	0.30 RPM	56.67 RPM

ChIP-Seq

Latimeria chalumnae was not studied using ChIP-Seq data.

EST

Latimeria chalumnae was not studied using EST data.

TSS

Latimeria chalumnae was not studied using FANTOM5 data.

Lab

retro_lcha_65 was not experimentally validated.

Homology

Retrocopy orthology:

Latimeria chalumnae 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016604	1 retrocopy	retro_amel_1421,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Latimeria chalumnae	ENSLACG00000015565	1 retrocopy	retro_lcha_65 ,
Microcebus murinus	ENSMICG00000004110	2 retrocopies	retro_mmur_183, retro_mmur_197,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Macaca mulatta	ENSMMUG00000000193	1 retrocopy	retro_mmul_1590,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Nomascus leucogenys	ENSNLEG00000009913	1 retrocopy	retro_nleu_1845,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Tupaia belangeri	ENSTBEG00000017492	6 retrocopies	retro_tbel_1604, retro_tbel_312, retro_tbel_3762, retro_tbel_4137, retro_tbel_4712, retro_tbel_798,