RetrogeneDB ID: retro_lcha_104

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH128305.1:100903..101298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3C
• Ensembl ID: ENSLACG00000004118
• Aliases: None
• Description: Histone H3 [Source:UniProtKB/TrEMBL;Acc:H3A4Q6]

Sequence

>retro_lcha_104
ATGGCTCATACAAAGCAGACTGCTCATAAATCCACTGGTGGGAAAGCTCCCCACAAGCAGCTCGCCACCCAGGCTGCACG
TAAGAGTTCTCCCTCAACAGGTGGAGTGAAAAAGCCTCATCGTTACAGGCCTGGTACTGTGGCTCTGCATGAGATCAGGC
GGTACCAGAAATCAACTGAGTTGCTGATCTGTAAATTGCCCTTCCAGCGCCTGTCCGTGAGATCGCACAGGACTTGAAAA
CAGACCTGAGGTTCCAGAGTGCATCCATAGGCACCCTGCAGGAGGCCAGCGAGGCTTATCTGGTGGGTCTCTTTGAAGAC
ACCAACCTTTGTGCCATTCATGCCAAGAGTCTCACCATCATGCCCAAAGATATCCAACTAGCCCGCAAGCTTAAA

Alignment

ORF - retro_lcha_104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.97 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MA.TKQTA.KSTGGKAP.KQLAT.AARKS.PSTGGVKKPHRYRPGTVAL.EIRRYQKSTELLI.KLPFQR
Retrocopy MAHTKQTAHKSTGGKAPHKQLATQAARKSSPSTGGVKKPHRYRPGTVALHEIRRYQKSTELLICKLPFQR

Parental  L-VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR
          L.VREIAQD.KTDLRFQSA.IG.LQEASEAYLVGLFEDTNLCAIHAK..TIMPKDIQLAR...
Retrocopy L<VREIAQDLKTDLRFQSASIGTLQEASEAYLVGLFEDTNLCAIHAKSLTIMPKDIQLARKLK

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	112.42 RPM
DRP000627_kidney	0.01 RPM	86.07 RPM
DRP000627_pectoral_fin	0.04 RPM	287.43 RPM
DRP000627_pelvic_fin	0.05 RPM	353.48 RPM
DRP000627_pharynx	0.00 RPM	36.67 RPM
DRP000627_tail_muscle	0.00 RPM	32.07 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_104 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 13 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Dasypus novemcinctus	ENSDNOG00000024843	2 retrocopies	retro_dnov_1624, retro_dnov_775,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266,
Homo sapiens	ENSG00000132475	11 retrocopies	retro_hsap_1212, retro_hsap_1552, retro_hsap_2180, retro_hsap_24, retro_hsap_2971, retro_hsap_3231, retro_hsap_3294, retro_hsap_3299, retro_hsap_389, retro_hsap_4236, retro_hsap_911,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104 ,
Loxodonta africana	ENSLAFG00000008083	3 retrocopies	retro_lafr_837, retro_lafr_959, retro_lafr_99,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Mustela putorius furo	ENSMPUG00000004555	4 retrocopies	retro_mputfur_389, retro_mputfur_82, retro_mputfur_99, retro_mputfur_990,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pan troglodytes	ENSPTRG00000009655	12 retrocopies	retro_ptro_1742, retro_ptro_1915, retro_ptro_2009, retro_ptro_2227, retro_ptro_2231, retro_ptro_2234, retro_ptro_2238, retro_ptro_2640, retro_ptro_2879, retro_ptro_631, retro_ptro_695, retro_ptro_830,
Tupaia belangeri	ENSTBEG00000016171	7 retrocopies	retro_tbel_3459, retro_tbel_3605, retro_tbel_3824, retro_tbel_3856, retro_tbel_4243, retro_tbel_4350, retro_tbel_674,