RetrogeneDB ID: retro_lcha_28

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126600.1:2833124..2833352(-)
• Located in intron of: ENSLACG00000018127

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM4
• Ensembl ID: ENSLACG00000015861
• Aliases: None
• Description: None

Sequence

>retro_lcha_28
ATGTTTCCACTGTCATTATTGAAGATGGTTCAGAATTATCCTATGTTAGTGGAGTTGAAGGATGGGGAAACGTACAGTGG
TCACTTAGTGAGCTGTGATAACTTCTCTCAGGTTGATGTTCATCTAGTTATCTGTACATCCAGGGATGGTGACAAATTTT
GGAGGATACATACAGTATGTAGCAGCACCATTAAATACCTATGAATTCCAGATGAAATTATTGACATC

Alignment

ORF - retro_lcha_28 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 55.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECYIRGSTIKYLR
          M.PLSLLK..QN.PMLVELK.GETY.GHLVSCDN........VICTSRDGDKFWR........STIKYL.
Retrocopy MFPLSLLKMVQNYPMLVELKDGETYSGHLVSCDNFSQVDVHLVICTSRDGDKFWRIHT--VCSSTIKYL*

Parental  IPDEIIDM
          IPDEIID.
Retrocopy IPDEIIDI

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	1.63 RPM
DRP000627_kidney	0.00 RPM	1.69 RPM
DRP000627_pectoral_fin	0.00 RPM	6.54 RPM
DRP000627_pelvic_fin	0.00 RPM	4.21 RPM
DRP000627_pharynx	0.00 RPM	1.19 RPM
DRP000627_tail_muscle	0.00 RPM	1.19 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_28 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014900	1 retrocopy	retro_cfam_1954,
Echinops telfairi	ENSETEG00000007762	2 retrocopies	retro_etel_1656, retro_etel_51,
Latimeria chalumnae	ENSLACG00000015861	1 retrocopy	retro_lcha_28 ,
Myotis lucifugus	ENSMLUG00000004010	1 retrocopy	retro_mluc_832,