RetrogeneDB ID: retro_lcha_29

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126620.1:950995..951406(-)
• Located in intron of: ENSLACG00000013972

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL14
• Ensembl ID: ENSLACG00000015639
• Aliases: None
• Description: None

Sequence

>retro_lcha_29
GTGTTCAAACGCTATGTCGAGATTGGTCGGGTTGCCTACATATCCTTTGGCCCACATGCTGGCAAGCTAGTAGCCATTGT
TGATGTTATTGACCAGAATAGGGCGCTGGTTGATGGCCCCTGCAGTGGTGTTAGAAGACAGGCTATGCCCTTCAAGTGTA
TGCAGCTCACAGATTTTGTCATCAAGATCCAACACAGCACTTGACAGAAGCACGTAAAAGCTGCCTGGGAAAAAGAGGAG
ATTAATGAGAAATGGGCAGCTTCAAGCTGGGCAAAGAAAATTGAAGCAAGAGAAAAGAAGGCAAAGATGACAGATTTTGA
CCGTTACAAGGTCATGAAGGCCAAGAAAATGAGGAACAAGATCATCAAACACGAAATTAAGAAACTTCAGAAGGAGGCTG
CCAAAAAGGCA

Alignment

ORF - retro_lcha_29 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.14 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFKRYVEIGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCSGVRRQAMPFKCMQLTDFVIKIQHRYQIP
          VFKRYVEIGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCSGVRRQAMPFKCMQLTDFVIKIQH.....
Retrocopy VFKRYVEIGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCSGVRRQAMPFKCMQLTDFVIKIQHST*QK

Parental  EVTDFWLVLVFKKKKKKKTWGKTLDKKKKKKKKKKANFLKNFHFIRTQSMRNKIIKHEIKKLQKEAAKKA
          .V...W.......K.....W.K.........KK.K..............MRNKIIKHEIKKLQKEAAKKA
Retrocopy HVKAAWEKEEINEKWAASSWAKKIEARE---KKAKMTDFDRYKVMKAKKMRNKIIKHEIKKLQKEAAKKA

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	445.25 RPM	43.10 RPM
DRP000627_kidney	457.84 RPM	28.23 RPM
DRP000627_pectoral_fin	694.05 RPM	67.28 RPM
DRP000627_pelvic_fin	774.90 RPM	71.13 RPM
DRP000627_pharynx	314.73 RPM	35.58 RPM
DRP000627_tail_muscle	208.77 RPM	22.41 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_29 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 27 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001709	4 retrocopies	retro_amel_1876, retro_amel_1933, retro_amel_296, retro_amel_660,
Canis familiaris	ENSCAFG00000005138	1 retrocopy	retro_cfam_31,
Callithrix jacchus	ENSCJAG00000017884	9 retrocopies	retro_cjac_1249, retro_cjac_1393, retro_cjac_1835, retro_cjac_2138, retro_cjac_2139, retro_cjac_2332, retro_cjac_2797, retro_cjac_3240, retro_cjac_630,
Cavia porcellus	ENSCPOG00000000711	1 retrocopy	retro_cpor_529,
Equus caballus	ENSECAG00000026813	2 retrocopies	retro_ecab_377, retro_ecab_743,
Echinops telfairi	ENSETEG00000012894	6 retrocopies	retro_etel_2117, retro_etel_2155, retro_etel_251, retro_etel_315, retro_etel_356, retro_etel_387,
Felis catus	ENSFCAG00000015655	4 retrocopies	retro_fcat_1000, retro_fcat_1457, retro_fcat_587, retro_fcat_671,
Homo sapiens	ENSG00000188846	6 retrocopies	retro_hsap_1015, retro_hsap_1047, retro_hsap_2796, retro_hsap_3104, retro_hsap_3352, retro_hsap_4777,
Gorilla gorilla	ENSGGOG00000025958	3 retrocopies	retro_ggor_122, retro_ggor_1945, retro_ggor_2272,
Latimeria chalumnae	ENSLACG00000015639	1 retrocopy	retro_lcha_29 ,
Microcebus murinus	ENSMICG00000009217	4 retrocopies	retro_mmur_1218, retro_mmur_1352, retro_mmur_279, retro_mmur_3,
Myotis lucifugus	ENSMLUG00000014429	4 retrocopies	retro_mluc_1294, retro_mluc_2263, retro_mluc_420, retro_mluc_563,
Monodelphis domestica	ENSMODG00000015262	2 retrocopies	retro_mdom_1499, retro_mdom_1939,
Mustela putorius furo	ENSMPUG00000017961	1 retrocopy	retro_mputfur_90,
Mus musculus	ENSMUSG00000025794	3 retrocopies	retro_mmus_2904, retro_mmus_2929, retro_mmus_3011,
Nomascus leucogenys	ENSNLEG00000005682	2 retrocopies	retro_nleu_763, retro_nleu_918,
Oryctolagus cuniculus	ENSOCUG00000010309	3 retrocopies	retro_ocun_410, retro_ocun_464, retro_ocun_656,
Pan troglodytes	ENSPTRG00000011963	4 retrocopies	retro_ptro_1893, retro_ptro_2100, retro_ptro_2135, retro_ptro_713,
Pteropus vampyrus	ENSPVAG00000013914	7 retrocopies	retro_pvam_1108, retro_pvam_1413, retro_pvam_246, retro_pvam_446, retro_pvam_683, retro_pvam_903, retro_pvam_904,
Rattus norvegicus	ENSRNOG00000019007	4 retrocopies	retro_rnor_2268, retro_rnor_2620, retro_rnor_415, retro_rnor_591,
Sorex araneus	ENSSARG00000003974	2 retrocopies	retro_sara_349, retro_sara_504,
Sarcophilus harrisii	ENSSHAG00000001591	5 retrocopies	retro_shar_397, retro_shar_539, retro_shar_696, retro_shar_737, retro_shar_788,
Sus scrofa	ENSSSCG00000011272	2 retrocopies	retro_sscr_521, retro_sscr_63,
Ictidomys tridecemlineatus	ENSSTOG00000021460	1 retrocopy	retro_itri_946,
Tarsius syrichta	ENSTSYG00000002161	5 retrocopies	retro_tsyr_1036, retro_tsyr_1404, retro_tsyr_176, retro_tsyr_361, retro_tsyr_956,
Tursiops truncatus	ENSTTRG00000006708	1 retrocopy	retro_ttru_113,
Xenopus tropicalis	ENSXETG00000022018	1 retrocopy	retro_xtro_3,