RetrogeneDB ID: retro_lcha_59

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127044.1:249628..250125(-)
• Located in intron of: ENSLACG00000022591

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000012468
• Aliases: None
• Description: None

Sequence

>retro_lcha_59
AGAGTTATTGATGGAGCCAAGCATGCTCTTAAGTTCTGTACCACAGAGGAAGAAGAAAGCGTTTACCTCTGATGGCCTGA
AGGGATAGAATGGCAATACTGAAAGAAGTGTGGGAAGTGTGGGCTCCTGCTCTTATACCAGCACCAATAGAAAAATGTCC
CAGTCACGTTTATAGTGGACAGAGCTGTGGTCAAGTTTGGCCAGGGATTCAGAAGCATGTATGCCTACAACCCGAAACAA
GAGCCCCCAAAGAAGGTAATGATGACCAAACGCGCCAAAGACATGGTCAAGTTTAGCTCCGTGACTGCGTCAACCATTGA
TGAGGAAGAAGAGGAAATTGAGGCGTGAGAAATAGCAGACTCATATGCACAGAATGCTAAGGTGATTAAGAATAGCTGGA
GTATAAGGGAATGAGCAAGCAGTGGCTACAAGAACTGGCTGAGTTGGAGGCAAAGAAAGCCAAAATGAAAGGCATGCTGA
TTGACAACCAGTTCAAG

Alignment

ORF - retro_lcha_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.63 %
• Parental protein coverage: 74.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RVIDGAKHAHKFCTTEEEESVYLRRPEGIERQYRKKCGKCGLLLFYQHQQKNAPVTFIVDGAVVKFGQGF
          RVIDGAKHA.KFCTTEEEESVYL..PEGIE.QY.KKCGKCGLLL.YQHQ.KN.PVTFIVD.AVVKFGQGF
Retrocopy RVIDGAKHALKFCTTEEEESVYL*WPEGIEWQY*KKCGKCGLLLLYQHQ*KNVPVTFIVDRAVVKFGQGF

Parental  GSTYVYNPKQEPPKKVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREIADSYAQNAKVIEKQ-LERKGMS
          .S.Y.YNPKQEPPKKVMMTKR.KDM.KFSSVT.STIDEEEEEIEA.EIADSYAQNAKVI....LE.KGMS
Retrocopy RSMYAYNPKQEPPKKVMMTKRAKDMVKFSSVTASTIDEEEEEIEA*EIADSYAQNAKVIKNS<LEYKGMS

Parental  KRRLQELAELEAKKAKMKGTLIDNQFK
          K..LQELAELEAKKAKMKG.LIDNQFK
Retrocopy KQWLQELAELEAKKAKMKGMLIDNQFK

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	27.00 RPM
DRP000627_kidney	0.00 RPM	24.78 RPM
DRP000627_pectoral_fin	0.00 RPM	43.51 RPM
DRP000627_pelvic_fin	0.00 RPM	55.27 RPM
DRP000627_pharynx	0.00 RPM	18.78 RPM
DRP000627_tail_muscle	0.02 RPM	15.37 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_59 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 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005111	1 retrocopy	retro_cjac_311,
Homo sapiens	ENSG00000018610	1 retrocopy	retro_hsap_4044,
Gorilla gorilla	ENSGGOG00000013324	1 retrocopy	retro_ggor_2711,
Latimeria chalumnae	ENSLACG00000012468	1 retrocopy	retro_lcha_59 ,
Myotis lucifugus	ENSMLUG00000015751	1 retrocopy	retro_mluc_72,
Macaca mulatta	ENSMMUG00000022665	1 retrocopy	retro_mmul_2333,
Mus musculus	ENSMUSG00000006423	1 retrocopy	retro_mmus_1715,
Nomascus leucogenys	ENSNLEG00000014862	1 retrocopy	retro_nleu_2057,
Otolemur garnettii	ENSOGAG00000012474	1 retrocopy	retro_ogar_145,
Pongo abelii	ENSPPYG00000020670	1 retrocopy	retro_pabe_177,
Pan troglodytes	ENSPTRG00000022224	1 retrocopy	retro_ptro_104,
Sorex araneus	ENSSARG00000003163	1 retrocopy	retro_sara_5,
Sarcophilus harrisii	ENSSHAG00000006319	1 retrocopy	retro_shar_16,
Ictidomys tridecemlineatus	ENSSTOG00000011579	1 retrocopy	retro_itri_103,
Tarsius syrichta	ENSTSYG00000008043	1 retrocopy	retro_tsyr_634,
Tursiops truncatus	ENSTTRG00000013101	2 retrocopies	retro_ttru_231, retro_ttru_77,