RetrogeneDB ID: retro_lcha_78

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127241.1:238997..239393(+)
• Located in intron of: ENSLACG00000022641

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000007042
• Aliases: None
• Description: None

Sequence

>retro_lcha_78
AGTGTTGTTTTGAGCCAGTCTAGTGAAGAAGTAAAAAAAGCTGGAGAATCCCTGAGACTAAAATGTAGTCTCAGTGGGTT
TGATGTTAGCAGCTATGATATGTATCGGTACAGACAGGCTCCTGGAAAAGGGCTGGAATGGTTGGTTAAGTTTTGGAGTT
CCTCTGACAATCATTATTCCCCTTCAATCCAAGGACGGTTCACTGCCTCTAAGGAAAACTCTAATTTCTATTTACAAATG
AAGAATCTGGGAGTTGAAGACATGGCCATGTATTACTGTGCAAGGAGAGACCCACAGTGATAGACAGTATCCCGATGCTG
AACAAAAACCTATAACACATCTACACTCAGCTGTGCAGGTGGCAGCAGGAAACTGAGAAACTATGAACCACTAACT

Alignment

ORF - retro_lcha_78 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVVLSQSSEEVKKAEESLKLKCILSGFDVNSYDMYWYRKAPGKGLEWLVRYYSSSSNHYSPSIQGRFTAS
          .VVLSQSSEEVKKA.ESL.LKC.LSGFDV.SYDMY.YR.APGKGLEWLV...SSS.NHYSPSIQGRFTAS
Retrocopy SVVLSQSSEEVKKAGESLRLKCSLSGFDVSSYDMYRYRQAPGKGLEWLVKFWSSSDNHYSPSIQGRFTAS

Parental  KDSSNFYLQMNSLRVEDMAMYYCARREPHTPAIVRLFSHTVYRGGGGGGGGGGSFHFYAVLT
          K..SNFYLQM..L.VEDMAMYYCARR.P......R....T.........GG......Y..LT
Retrocopy KENSNFYLQMKNLGVEDMAMYYCARRDPQ**TVSRC*TKTYNTSTLSCAGGSRKLRNYEPLT

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	0.00 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	0.00 RPM	0.00 RPM
DRP000627_tail_muscle	0.00 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_78 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000007042	1 retrocopy	retro_lcha_78 ,