RetrogeneDB ID: retro_lcha_127

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH131904.1:22765..23050(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRB
• Ensembl ID: ENSLACG00000004465
• Aliases: None
• Description: None

Sequence

>retro_lcha_127
GTATCTGCTACAAGTTGTTTGTTGGAAGGCTTTCGGAAATGGTACTAGAATGCAGCTGGTTTTAAAAAACTTGGGCTAAT
GCAGGATGATACAATGTATGAAGATGCTGATGTGAAAGAGGCTTTGAAAAGGATTCCAGAGAATGTTTACAATAATTGAA
TGTTCCACATTAAGAGAGCGCTAGACATATCTAGGAAGCACCAGATTCTTTCAAAAGAACAGTGGACAAAATATGAGGAG
AATGTTCCATACCTAGAGCTGTACTTGAAAGAAGTTATCCAAAAA

Alignment

ORF - retro_lcha_127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 82.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSATSRLLEGFRKWYYNAAGFNKLEGLMRDDTMYEDADVKEALKRIPENVYNDRMFRIKRALDLSLKHQI
          VSATS.LLEGFRKWY.NAAGF.KL.GLM.DDTMYEDADVKEALKRIPENVYN..MF.IKRALD.S.KHQI
Retrocopy VSATSCLLEGFRKWY*NAAGFKKL-GLMQDDTMYEDADVKEALKRIPENVYNN*MFHIKRALDISRKHQI

Parental  LPKEQWTKYEEDVPYLGPYLKEVIRE
          L.KEQWTKYEE.VPYL..YLKEVI..
Retrocopy LSKEQWTKYEENVPYLELYLKEVIQK

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	0.05 RPM	31.96 RPM
DRP000627_kidney	0.03 RPM	49.34 RPM
DRP000627_pectoral_fin	0.02 RPM	50.72 RPM
DRP000627_pelvic_fin	0.00 RPM	69.55 RPM
DRP000627_pharynx	0.05 RPM	36.01 RPM
DRP000627_tail_muscle	0.02 RPM	25.89 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_127 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 30 parental genes, and 111 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007287	1 retrocopy	retro_amel_985,
Bos taurus	ENSBTAG00000001521	3 retrocopies	retro_btau_1641, retro_btau_374, retro_btau_417,
Canis familiaris	ENSCAFG00000009449	4 retrocopies	retro_cfam_1504, retro_cfam_1509, retro_cfam_1531, retro_cfam_792,
Choloepus hoffmanni	ENSCHOG00000007884	22 retrocopies	retro_chof_1256, retro_chof_1271, retro_chof_1468, retro_chof_1662, retro_chof_1888, retro_chof_2017, retro_chof_2170, retro_chof_2332, retro_chof_2528, retro_chof_2536, retro_chof_2554, retro_chof_257, retro_chof_2684, retro_chof_394, retro_chof_524, retro_chof_599, retro_chof_635, retro_chof_654, retro_chof_699, retro_chof_766, retro_chof_773, retro_chof_975,
Callithrix jacchus	ENSCJAG00000020560	2 retrocopies	retro_cjac_2206, retro_cjac_894,
Cavia porcellus	ENSCPOG00000012149	2 retrocopies	retro_cpor_1086, retro_cpor_866,
Dasypus novemcinctus	ENSDNOG00000017312	8 retrocopies	retro_dnov_1109, retro_dnov_1163, retro_dnov_1706, retro_dnov_2410, retro_dnov_2518, retro_dnov_369, retro_dnov_608, retro_dnov_798,
Equus caballus	ENSECAG00000009780	1 retrocopy	retro_ecab_1116,
Erinaceus europaeus	ENSEEUG00000001312	1 retrocopy	retro_eeur_224,
Felis catus	ENSFCAG00000026302	5 retrocopies	retro_fcat_1292, retro_fcat_178, retro_fcat_1780, retro_fcat_378, retro_fcat_558,
Homo sapiens	ENSG00000156467	2 retrocopies	retro_hsap_3261, retro_hsap_4838,
Gorilla gorilla	ENSGGOG00000026528	1 retrocopy	retro_ggor_3017,
Latimeria chalumnae	ENSLACG00000004465	1 retrocopy	retro_lcha_127 ,
Loxodonta africana	ENSLAFG00000002542	1 retrocopy	retro_lafr_727,
Myotis lucifugus	ENSMLUG00000007182	1 retrocopy	retro_mluc_1601,
Macaca mulatta	ENSMMUG00000008804	3 retrocopies	retro_mmul_2053, retro_mmul_2065, retro_mmul_2581,
Mus musculus	ENSMUSG00000021520	4 retrocopies	retro_mmus_1175, retro_mmus_1628, retro_mmus_2610, retro_mmus_514,
Nomascus leucogenys	ENSNLEG00000026670	1 retrocopy	retro_nleu_1357,
Oryctolagus cuniculus	ENSOCUG00000008113	3 retrocopies	retro_ocun_1149, retro_ocun_345, retro_ocun_570,
Otolemur garnettii	ENSOGAG00000004302	1 retrocopy	retro_ogar_1451,
Ochotona princeps	ENSOPRG00000008892	2 retrocopies	retro_opri_109, retro_opri_688,
Pongo abelii	ENSPPYG00000018763	2 retrocopies	retro_pabe_2703, retro_pabe_3762,
Pteropus vampyrus	ENSPVAG00000012321	1 retrocopy	retro_pvam_498,
Rattus norvegicus	ENSRNOG00000024967	1 retrocopy	retro_rnor_290,
Sorex araneus	ENSSARG00000002999	3 retrocopies	retro_sara_460, retro_sara_52, retro_sara_704,
Ictidomys tridecemlineatus	ENSSTOG00000008017	1 retrocopy	retro_itri_46,
Tupaia belangeri	ENSTBEG00000002453	28 retrocopies	retro_tbel_1046, retro_tbel_1268, retro_tbel_1357, retro_tbel_1568, retro_tbel_1583, retro_tbel_1656, retro_tbel_1688, retro_tbel_169, retro_tbel_1858, retro_tbel_2106, retro_tbel_2217, retro_tbel_248, retro_tbel_2675, retro_tbel_274, retro_tbel_2883, retro_tbel_2885, retro_tbel_2893, retro_tbel_2942, retro_tbel_3129, retro_tbel_3156, retro_tbel_3291, retro_tbel_3492, retro_tbel_3662, retro_tbel_4334, retro_tbel_4539, retro_tbel_457, retro_tbel_517, retro_tbel_784,
Tarsius syrichta	ENSTSYG00000010502	2 retrocopies	retro_tsyr_1114, retro_tsyr_898,
Tursiops truncatus	ENSTTRG00000007348	3 retrocopies	retro_ttru_1106, retro_ttru_501, retro_ttru_754,
Drosophila melanogaster	FBgn0030733	1 retrocopy	retro_dmel_22,