RetrogeneDB ID: retro_lcha_85

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127493.1:471743..472508(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000010078
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BDH1
• Ensembl ID: ENSLACG00000016430
• Aliases: None
• Description: None

Sequence

>retro_lcha_85
CAGGATAAAGGGAGCGATGGTGTTAACCAACTGGATAACTTGAAGAGCGAGCGGTTAAAAACAGTCCAGTTAAACGTCTG
TGAGGATGAAGAAGTAGAAGCAGCAGTGCGGTTTGTTCAAGGGAATTTAAAGGATCCAGAGAAAGGGCTGTGGGGTGTAG
TGAATAATGCAGGAATCTCCACCTTTGGAGAGGTGGAATTTATAAGCATGGAAACATACAAAGAGATAGCTGAAGTTAAT
CTCTGGGGGACAGTCCAAGTGACCAAGGCCTTCCTTCCTCTCATCCGCAGAGCCAAAGGCCGTGTTGTTAATATCACCAG
TATGTTGGGACGGATGGCTAACCCAGCACGCTCCCCTTACTGCGTCACCAAGTTTGGAGTGGAAGCATTTTCAGACTGCC
TGAGATATGAGATGCACCGCTGGGGAGTCAAAGTCAGCATCGTGGAACCTGGGAACTTCATTGCTGCCACAAGTCTCTAC
AGCCCGGAGCGGATCAAAGTGATCGCTGAAAAGATGTGGAGCGACCTTCCTGAGGTGGTCCGCAACGACTACGGCAGGAA
ATACTTCGATGAGCAGATTGCTAAGATGCACTCGTACTGTAACAGTGGAGCAACAGACACATCCCCTGTCATCGATGATG
TCACTCATGCTCTGACCGCGCCTTCCCCATACATCCGCTACCACCCCATGGACTATTACTGGTGGCTGAGAATGCAGATC
ATAACTCATATGCCTGCTGCAATTTCAGACCGAATTTATATCTAT

Alignment

ORF - retro_lcha_85 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.86 %
• Parental protein coverage: 79.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDKGSDGVNQLDNLKSERLKTVQLNVCEDEEVEAAVQFVQGNLKDPEKGLWGVVNNAGISTFGEVEFTSM
          .DKGSDGVNQLDNLKSERLKTVQLNVCEDEEVEAAV.FVQGNLKDPEKGLWGVVNNAGISTFGEVEF.SM
Retrocopy QDKGSDGVNQLDNLKSERLKTVQLNVCEDEEVEAAVRFVQGNLKDPEKGLWGVVNNAGISTFGEVEFISM

Parental  ETYKEVAEVNLWGTVRVTKAFLPLIRRAKGRVVNITSMLGRMANPARSPYCVTKFGVEAFSDCLRYEMHR
          ETYKE.AEVNLWGTV.VTKAFLPLIRRAKGRVVNITSMLGRMANPARSPYCVTKFGVEAFSDCLRYEMHR
Retrocopy ETYKEIAEVNLWGTVQVTKAFLPLIRRAKGRVVNITSMLGRMANPARSPYCVTKFGVEAFSDCLRYEMHR

Parental  WGIKVSIVEPGNFIAATSLYSPERIKVIAEKMWSDLPEVVRNDYGKKYFDEQIAKMHSYCNSGATDTSPV
          WG.KVSIVEPGNFIAATSLYSPERIKVIAEKMWSDLPEVVRNDYG.KYFDEQIAKMHSYCNSGATDTSPV
Retrocopy WGVKVSIVEPGNFIAATSLYSPERIKVIAEKMWSDLPEVVRNDYGRKYFDEQIAKMHSYCNSGATDTSPV

Parental  IDDVTHALTAPSPYTRYHPMDYYWWLRMQIITHMPAAISDRIYIY
          IDDVTHALTAPSPY.RYHPMDYYWWLRMQIITHMPAAISDRIYIY
Retrocopy IDDVTHALTAPSPYIRYHPMDYYWWLRMQIITHMPAAISDRIYIY

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	0.19 RPM	2.34 RPM
DRP000627_kidney	0.11 RPM	3.30 RPM
DRP000627_pectoral_fin	0.16 RPM	1.05 RPM
DRP000627_pelvic_fin	0.03 RPM	1.79 RPM
DRP000627_pharynx	0.21 RPM	2.71 RPM
DRP000627_tail_muscle	0.19 RPM	2.92 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_85 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014536	1 retrocopy	retro_acar_55,
Latimeria chalumnae	ENSLACG00000016430	1 retrocopy	retro_lcha_85 ,