RetrogeneDB ID: retro_lcha_89

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127556.1:607279..607765(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRI
• Ensembl ID: ENSLACG00000000210
• Aliases: None
• Description: None

Sequence

>retro_lcha_89
GGCTACCCTGGAGGCTTTGGTACAACATGTGGTGCTGCTCCTGGAGCCCCTGGAGTCTGTGGGTAGGCACAGGACTCCTT
GTTTGGTTATTTTTCTGCAGTAGCTGGTTCAGATGGACAGACTGATGCTTCAGAACTGCAGATGTGTCTCACCCAATCTG
GCATTAGTGGAAGTTATACACCATTCAATTTGGAAACCTGCAGGCTTATGATTGGCATGTTGGGTAGAGGCTTTTCTGAC
AAAATGGGCTTCAAGGAATTTAAAGAGCTCTGAGCTGCATTAAATGGTTGGAAACAGAACTTTATGGGTTTTGACAGAGA
TCAGAATAGCATAGTACAGCCTCAGGAACTACACCAAGCCATTTCTTCCAAGGGGTCTAGACCGAGTCCTCAAGCATCCA
GCGTGATAGCAAATCGCTACAGCAGCAATGGAAGGGTCACATTTGTCGATTTTGTGGCTTGCTGTGTGAAACGTCGTGTC
TTAACT

Alignment

ORF - retro_lcha_89 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 80.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYPGGFGATYGAAPGAPGIHGQAQDPLFGYFSAVAGSDGQIDASELQMCLTQSGISGGYKPFNLETCRLM
          GYPGGFG.T.GAAPGAPG..G.AQD.LFGYFSAVAGSDGQ.DASELQMCLTQSGISG.Y.PFNLETCRLM
Retrocopy GYPGGFGTTCGAAPGAPGVCG*AQDSLFGYFSAVAGSDGQTDASELQMCLTQSGISGSYTPFNLETCRLM

Parental  IGMLDRDFSGKMGFNEFKELWTALNGWKQNFMGFDRDQSGTVEPQELHQAITSMGYRLSPQAFNVIVHRY
          IGML.R.FS.KMGF.EFKEL..ALNGWKQNFMGFDRDQ...V.PQELHQAI.S.G.R.SPQA..VI..RY
Retrocopy IGMLGRGFSDKMGFKEFKEL*AALNGWKQNFMGFDRDQNSIVQPQELHQAISSKGSRPSPQASSVIANRY

Parental  GINGKVAFDDFVACCVKLRVLT
          ..NG.V.F.DFVACCVK.RVLT
Retrocopy SSNGRVTFVDFVACCVKRRVLT

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	2.21 RPM
DRP000627_kidney	0.00 RPM	1.55 RPM
DRP000627_pectoral_fin	0.00 RPM	3.87 RPM
DRP000627_pelvic_fin	0.00 RPM	8.07 RPM
DRP000627_pharynx	0.02 RPM	0.48 RPM
DRP000627_tail_muscle	0.00 RPM	0.49 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_89 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001855	1 retrocopy	retro_cfam_498,
Cavia porcellus	ENSCPOG00000010096	1 retrocopy	retro_cpor_216,
Latimeria chalumnae	ENSLACG00000000210	1 retrocopy	retro_lcha_89 ,
Loxodonta africana	ENSLAFG00000027380	2 retrocopies	retro_lafr_1186, retro_lafr_487,
Monodelphis domestica	ENSMODG00000010355	1 retrocopy	retro_mdom_782,
Mustela putorius furo	ENSMPUG00000018313	1 retrocopy	retro_mputfur_1147,
Pteropus vampyrus	ENSPVAG00000007438	2 retrocopies	retro_pvam_1112, retro_pvam_734,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237,
Ictidomys tridecemlineatus	ENSSTOG00000004372	1 retrocopy	retro_itri_607,
Tupaia belangeri	ENSTBEG00000004434	1 retrocopy	retro_tbel_4493,
Tarsius syrichta	ENSTSYG00000014640	1 retrocopy	retro_tsyr_1832,
Xenopus tropicalis	ENSXETG00000008793	1 retrocopy	retro_xtro_25,