RetrogeneDB ID: retro_lcha_48

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126924.1:1315747..1315976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA2
• Ensembl ID: ENSLACG00000005796
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 [Source:UniProtKB/TrEMBL;Acc:H3AA68]

Sequence

>retro_lcha_48
ATGTCAGAGCTCACAGAGCAGCCGGGTGGGGTCCGAGAATTTATTCAGCAACAAGTGATAATGAAGCAAGCACATCCTGG
CTCCCCCATCTTGATCAGAGAGTGCTCCGGCATTCTGCCCAAACTCTGGGCCCGATATGAGTTCAGGAAAGGAGAAGAGT
ACACCATTAGCCAACCTGGACTCAGAGCAGCTGACCAAGGCTCTGGAGTCTCCCATCAAGAGCAAAGTG

Alignment

ORF - retro_lcha_48 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 80.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LCQRSQSSQGVREFIEQQYVTLKQANPDFPILIRECSGIQPKLWARYEF-GKEKSVPLHNLNSEQVAKAL
          .........GVREFI.QQ.V..KQA.P..PILIRECSGI.PKLWARYEF.GKEKS.PL.NL.SEQ..KAL
Retrocopy MSELTEQPGGVREFIQQQ-VIMKQAHPGSPILIRECSGILPKLWARYEF>GKEKSTPLANLDSEQLTKAL

Parental  ESVIKSKV
          ES.IKSKV
Retrocopy ESPIKSKV

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	0.00 RPM	25.07 RPM
DRP000627_kidney	0.00 RPM	40.64 RPM
DRP000627_pectoral_fin	0.00 RPM	35.47 RPM
DRP000627_pelvic_fin	0.00 RPM	40.76 RPM
DRP000627_pharynx	0.00 RPM	27.87 RPM
DRP000627_tail_muscle	0.00 RPM	18.78 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_48 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015041	2 retrocopies	retro_btau_124, retro_btau_151,
Canis familiaris	ENSCAFG00000005861	1 retrocopy	retro_cfam_1343,
Callithrix jacchus	ENSCJAG00000016525	1 retrocopy	retro_cjac_3326,
Cavia porcellus	ENSCPOG00000009178	2 retrocopies	retro_cpor_1045, retro_cpor_1290,
Latimeria chalumnae	ENSLACG00000005796	1 retrocopy	retro_lcha_48 ,
Mus musculus	ENSMUSG00000014294	1 retrocopy	retro_mmus_2579,
Nomascus leucogenys	ENSNLEG00000009325	1 retrocopy	retro_nleu_67,
Otolemur garnettii	ENSOGAG00000027727	1 retrocopy	retro_ogar_1633,
Pongo abelii	ENSPPYG00000015860	1 retrocopy	retro_pabe_938,
Rattus norvegicus	ENSRNOG00000017571	1 retrocopy	retro_rnor_262,
Sus scrofa	ENSSSCG00000014371	1 retrocopy	retro_sscr_48,
Tupaia belangeri	ENSTBEG00000005978	1 retrocopy	retro_tbel_2688,