RetrogeneDB ID: retro_lcha_42

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126753.1:1372255..1372598(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000000234
• Aliases: None
• Description: None

Sequence

>retro_lcha_42
TATATCTACACTTGCATGGACAACCTTTCTTGCCACTGGCTGGAAAAGGTTATAGCAAAATTAGATGGAGCTAAATATAG
TATAGTTGTGTCTTCTTGCATAGCTACTGTAGTTACAATAGCACACTTGTTAAAAAGTAGGGAATCATATTTTGGTTAAA
AAAAACATATATGGAGAAACCAACCATTTTTTTACTGACTTTTGCAAAAAAATGGGGACAGAGATTTCTGATGCTTCCTT
CACAAATCCCATGGATATGCAGAAAAATCTGCCTCAGAACACAAACATTATGAGGATTGAGCTTCCCTTCAACCCTTACA
CAAGGGCCATTGATGTCAATGCT

Alignment

ORF - retro_lcha_42 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.09 %
• Parental protein coverage: 60.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YIYTRMDNPSRHGLEQVVGKLDGAKYSIAVSSGMAAVAVIAHLLKT-GDHILVEENIYGGTYHYFNDFCK
          YIYT.MDN.S.H.LE.V..KLDGAKYSI.VSS..A.V..IAHLLK..G.HILV...IYG.T.H.F.DFCK
Retrocopy YIYTCMDNLSCHWLEKVIAKLDGAKYSIVVSSCIATVVTIAHLLKS>GNHILVXXXIYGETNHFFTDFCK

Parental  KMGTQISDADFTNPSEVIKKLCQNTKIVWLESPSNPYTRVIDINA
          KMGT.ISDA.FTNP....K.L.QNT.I...E.P.NPYTR.ID.NA
Retrocopy KMGTEISDASFTNPMDMQKNLPQNTNIMRIELPFNPYTRAIDVNA

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	0.38 RPM
DRP000627_kidney	0.00 RPM	0.28 RPM
DRP000627_pectoral_fin	0.00 RPM	9.35 RPM
DRP000627_pelvic_fin	0.00 RPM	6.75 RPM
DRP000627_pharynx	0.00 RPM	0.01 RPM
DRP000627_tail_muscle	0.00 RPM	0.28 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_42 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014791	1 retrocopy	retro_btau_1577,
Latimeria chalumnae	ENSLACG00000000234	1 retrocopy	retro_lcha_42 ,
Ictidomys tridecemlineatus	ENSSTOG00000000202	1 retrocopy	retro_itri_922,