RetrogeneDB ID: retro_lcha_73

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127212.1:646327..646582(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSLACG00000002456
• Aliases: None
• Description: None

Sequence

>retro_lcha_73
AGTTTACCTTTGAATCCTAAACCCTTTCTTAATGGGTTGGCTGGGAAACCAGTGATGGTCAAGTTGAAATGGGGTATGGA
ATACAAAGGTTACTTGGTGTTTCTGGATGGATACATGAACATGCAACTTGCAAACACAGAAGAATACATCGACGGAGCAT
TGTCAGGCCATTTAGGAGAAGTCCTTATAAGATGTAACAATGTGCTTTATATCAGAGGTGTTGAAGAGGAAGAAGAAGAT
GGAGAAATGAGAGAA

Alignment

ORF - retro_lcha_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.47 %
• Parental protein coverage: 72.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLY
          SLPLNPKPFLNGL.GKPVMVKLKWGMEYKGYLV..DGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLY
Retrocopy SLPLNPKPFLNGLAGKPVMVKLKWGMEYKGYLVFLDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLY

Parental  IRGVEEEEEDGEMRE
          IRGVEEEEEDGEMRE
Retrocopy IRGVEEEEEDGEMRE

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	0.06 RPM	6.10 RPM
DRP000627_kidney	0.00 RPM	5.63 RPM
DRP000627_pectoral_fin	0.02 RPM	13.91 RPM
DRP000627_pelvic_fin	0.00 RPM	14.61 RPM
DRP000627_pharynx	0.04 RPM	7.35 RPM
DRP000627_tail_muscle	0.04 RPM	6.12 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_73 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 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Canis familiaris	ENSCAFG00000006395	6 retrocopies	retro_cfam_110, retro_cfam_1975, retro_cfam_372, retro_cfam_619, retro_cfam_742, retro_cfam_763,
Callithrix jacchus	ENSCJAG00000002705	2 retrocopies	retro_cjac_1705, retro_cjac_3039,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Latimeria chalumnae	ENSLACG00000002456	1 retrocopy	retro_lcha_73 ,