RetrogeneDB ID: retro_lcha_56

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127028.1:652320..652704(-)
• Located in intron of: ENSLACG00000011600

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000014539
• Aliases: None
• Description: None

Sequence

>retro_lcha_56
GCTGGCCATGAGATTGGCATTATGGAAAAGATGGTCAGAGACTGAATAAAGATGAAGCAGACGTTAAAAGAAATGGTGAA
GACAAAGCGCACTCACCATAGGAATGTGCAGTCATTTGCAGCCTTGGAGGTTGATCTAAATGAATGGGTACAACAGAGCC
GGCAGAATGGCTACATTGTGACAAGGAATGCCATCAGATTGTGGACACTAAAGATAGCAAAGGAAGAAAAGTACAAGACA
GATGCAAGCAGTATCTTTGTAGCCTCTGCTGGTTGGTGCACCCGTTTTATGGAGAGACATGGACTAACTATACAACAACG
AACCAAGATGGTGCAGAAACTGCCAAAGGATTTGGAGATGAAAGTTGATAGTTTCCTTGTTTGC

Alignment

ORF - retro_lcha_56 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.16 %
• Parental protein coverage: 75.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGREFGIMEKMIRDWRKTNETLEEMAKMKCANCGNMQSFVALEVDLNEWVLQSQQNGYIVTRNAIRSWAL
          AG.E.GIMEKM.RD..K...TL.EM.K.K.....N.QSF.ALEVDLNEWV.QS.QNGYIVTRNAIR.W.L
Retrocopy AGHEIGIMEKMVRD*IKMKQTLKEMVKTKRTHHRNVQSFAALEVDLNEWVQQSRQNGYIVTRNAIRLWTL

Parental  KMAKEEKYKTDGSSTFAASAGWCTCFMGSLSECIRKMKDAWESIPD--QMIHCSFLKC
          K.AKEEKYKTD.SS.F.ASAGWCT.FM......I..........P....M...SFL.C
Retrocopy KIAKEEKYKTDASSIFVASAGWCTRFMERHGLTIQQRTKMVQKLPKDLEMKVDSFLVC

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	0.05 RPM	0.00 RPM
DRP000627_kidney	0.00 RPM	0.00 RPM
DRP000627_pectoral_fin	0.00 RPM	0.00 RPM
DRP000627_pelvic_fin	0.00 RPM	0.00 RPM
DRP000627_pharynx	0.01 RPM	0.00 RPM
DRP000627_tail_muscle	0.02 RPM	0.00 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_56 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033914	1 retrocopy	retro_cjac_2779,
Dipodomys ordii	ENSDORG00000006822	1 retrocopy	retro_dord_612,
Erinaceus europaeus	ENSEEUG00000014393	1 retrocopy	retro_eeur_21,
Latimeria chalumnae	ENSLACG00000014539	1 retrocopy	retro_lcha_56 ,
Mus musculus	ENSMUSG00000040596	1 retrocopy	retro_mmus_2572,
Otolemur garnettii	ENSOGAG00000007615	1 retrocopy	retro_ogar_2784,
Tarsius syrichta	ENSTSYG00000011078	1 retrocopy	retro_tsyr_1983,