RetrogeneDB ID: retro_lcha_126

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH131319.1:60515..61248(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000000522
• Aliases: None
• Description: None

Sequence

>retro_lcha_126
AGGGCTCCACAACTGACCGTCAGTGATACGATGGCCGAAGATATAAAGAACATACATGCTCTTTTAGTGCAGCTTTCTTC
CAGTGTGTCGGAGGTTAAGCTGGCGATTCAAAATCTGCAGAATTCGCAGAATCGGCTGGGGCCAGGATAGCAGAGGTGGA
ACAGCGCGTCTCCAAGATCGAGGACGATGGGGTAGGAGAGAGTCAGCGACTACAGCAACTGGAACAGCGGCTTGCCGCTG
CCGCCGAGAAGATCGACGACTTGGAAAACAGGTTGAGGAGGAACAATGTTAGAATCATTGGATTTCCCGAGGGGGCTGAA
GAAGGGAATCCTGTGAATTTTTTTACAGAGGGTCCTCCCCGGGCTGCTGGATTTGGAGGAGGGGATGGCCCTAGAAATGG
AGAGGGCGCACCGGGCGCTGGGTCCACACCCTGAGCCGGGGCAGCGTCCGAGGGCGATTATAGTCAAGCTCCTGCGGTAT
CCCAACAGAGATCTCCTCTTTTGGGCTGCCAGGCTGAAGGGGACAGTGTTGTGGCAAGATCATTGGATTTCTATTTATCC
CGACTGGTCCAAGGAGTTGCAGTTTGAAGAAGCAGTGGTTCTGGGGCATCAGGAAGATTCTTCAGGAAAGGAAGATTAAG
TACGGGATGTTTTACCCCGCTACTTTGAAGATTACGGTTAACGGAGAGACTTTGGCCTTTACTAACCCAGAGGACGCCAG
GAAATTCCTCTCC

Alignment

ORF - retro_lcha_126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.87 %
• Parental protein coverage: 85.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RQMHFPISSNMIYHSNNLSRNRVQLTANVSEVKLAIPNLQNLQDQLG-ARIAEVEQHVSKIEGDGVGESQ
          R......S..M.....N.....VQL...VSEVKLAI.NLQN.Q..LG.ARIAEVEQ.VSKIE.DGVGESQ
Retrocopy RAPQLTVSDTMAEDIKNIHALLVQLSSSVSEVKLAIQNLQNSQNRLG<ARIAEVEQRVSKIEDDGVGESQ

Parental  RLWHLEQRLAAAAKWIDNLENRSRKNNVRIIGFPEGVEEGNPMN-FLQKVLPGLLDL-EGKILEMERAHW
          RL..LEQRLAAAA..ID.LENR.R.NNVRIIGFPEG.EEGNP.N.FLQ.VLPGLLDL.EG..LEMERAH.
Retrocopy RLQQLEQRLAAAAEKIDDLENRLRRNNVRIIGFPEGAEEGNPVN>FLQRVLPGLLDLEEGMALEMERAHR

Parental  ALGPHPAPGQSTRALIVKLLRYPTRDLLLQAAKLKGQVMWREHRISIFPDWSRELQ-LKRQWFWDIRKIL
          ALGPHP.PGQ..RA.IVKLLRYP.RDLL..AA.LKG.V.W..H.ISI.PDWS.ELQ.LK.QWFW.IRKIL
Retrocopy ALGPHPEPGQRPRAIIVKLLRYPNRDLLFWAARLKGTVLWQDHWISIYPDWSKELQ>LKKQWFWGIRKIL

Parental  REKKIKYGLFYPAILKITVNGEALAFTNPEDARKFLA
          .E.KIKYG.FYPA.LKITVNGE.LAFTNPEDARKFL.
Retrocopy QERKIKYGMFYPATLKITVNGETLAFTNPEDARKFLS

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	0.11 RPM
DRP000627_kidney	0.00 RPM	0.03 RPM
DRP000627_pectoral_fin	0.00 RPM	0.00 RPM
DRP000627_pelvic_fin	0.00 RPM	0.00 RPM
DRP000627_pharynx	0.00 RPM	0.03 RPM
DRP000627_tail_muscle	0.02 RPM	0.04 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_126 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
Latimeria chalumnae	ENSLACG00000000522	1 retrocopy	retro_lcha_126 ,
Latimeria chalumnae	ENSLACG00000002156	1 retrocopy	retro_lcha_107,