RetrogeneDB ID: retro_lcha_5

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH128885.1:58258..58696(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000002746
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rpl26 (3 of 3)
• Ensembl ID: ENSLACG00000007599
• Aliases: None
• Description: ribosomal protein L26 [Source:ZFIN;Acc:ZDB-GENE-040426-2117]

Sequence

>retro_lcha_5
ATGAAGTTCAACCCTCTTGTGATGTCTGATCGCAGCAAGAACCGTAAGAGGCACTTCAATGCTCCCTCTCACGTTCGCAG
AAAGATCATGTCTTCTCCTCTCTCCAAGGAGCTGAGACAGAAGTACAACGTACGCTCTATGCCCATCCGCAAGGACGATG
AAGTCCAGGTTGTCCGAGGACACTACAAAGGCCAGCAGATTGGCAAAGTTGTTCAAGTGTACAGAAAGAAATACGTCATC
TATATTGAACGTGTGCAGTGTGAAAAAGCCAATGGTACCACTGTCCATGTTGGCATTCACCCAAGCAAGGTGGTGATAAC
CAGACTAAAACTGGACAAAGATCGTAAGAAAATCCTAGAACGTAAAGCCAAATCTCGTCAAGTTGGCAAGGAGAAGGGCA
AATACAAGGAGGAAACCATTGAAAAAATGCAGGAGTAA

Alignment

ORF - retro_lcha_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFNPLVTSDRSKNRKRHFNAPSHVRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
          MKFNPLV.SDRSKNRKRHFNAPSHVRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
Retrocopy MKFNPLVMSDRSKNRKRHFNAPSHVRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV

Parental  VQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEETI
          VQVYRKKYVIYIERVQ.EKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEETI
Retrocopy VQVYRKKYVIYIERVQCEKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEETI

Parental  EKMQE
          EKMQE
Retrocopy EKMQE

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	1.14 RPM	680.63 RPM
DRP000627_kidney	1.12 RPM	818.32 RPM
DRP000627_pectoral_fin	13.42 RPM	1020.21 RPM
DRP000627_pelvic_fin	1.36 RPM	1102.93 RPM
DRP000627_pharynx	0.71 RPM	508.76 RPM
DRP000627_tail_muscle	0.60 RPM	330.41 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_5 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 97 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011270	7 retrocopies	retro_amel_1106, retro_amel_1477, retro_amel_172, retro_amel_272, retro_amel_560, retro_amel_788, retro_amel_887,
Dasypus novemcinctus	ENSDNOG00000002289	35 retrocopies	retro_dnov_1106, retro_dnov_1147, retro_dnov_1171, retro_dnov_1258, retro_dnov_1304, retro_dnov_1319, retro_dnov_1344, retro_dnov_1381, retro_dnov_1501, retro_dnov_1676, retro_dnov_1819, retro_dnov_1959, retro_dnov_2039, retro_dnov_2041, retro_dnov_2061, retro_dnov_2078, retro_dnov_2103, retro_dnov_2116, retro_dnov_2121, retro_dnov_2287, retro_dnov_2297, retro_dnov_2438, retro_dnov_2545, retro_dnov_2580, retro_dnov_2632, retro_dnov_300, retro_dnov_306, retro_dnov_467, retro_dnov_646, retro_dnov_666, retro_dnov_681, retro_dnov_760, retro_dnov_850, retro_dnov_970, retro_dnov_985,
Felis catus	ENSFCAG00000026949	1 retrocopy	retro_fcat_524,
Homo sapiens	ENSG00000037241	2 retrocopies	retro_hsap_586, retro_hsap_837,
Latimeria chalumnae	ENSLACG00000007599	2 retrocopies	retro_lcha_5 , retro_lcha_8,
Microcebus murinus	ENSMICG00000011312	10 retrocopies	retro_mmur_1020, retro_mmur_1144, retro_mmur_313, retro_mmur_327, retro_mmur_346, retro_mmur_412, retro_mmur_471, retro_mmur_623, retro_mmur_72, retro_mmur_75,
Myotis lucifugus	ENSMLUG00000009799	1 retrocopy	retro_mluc_1556,
Macaca mulatta	ENSMMUG00000003070	1 retrocopy	retro_mmul_676,
Mustela putorius furo	ENSMPUG00000012729	2 retrocopies	retro_mputfur_1624, retro_mputfur_190,
Oryctolagus cuniculus	ENSOCUG00000006172	4 retrocopies	retro_ocun_1015, retro_ocun_1224, retro_ocun_354, retro_ocun_845,
Procavia capensis	ENSPCAG00000002246	10 retrocopies	retro_pcap_137, retro_pcap_157, retro_pcap_188, retro_pcap_204, retro_pcap_337, retro_pcap_404, retro_pcap_419, retro_pcap_42, retro_pcap_422, retro_pcap_448,
Pteropus vampyrus	ENSPVAG00000003253	8 retrocopies	retro_pvam_1062, retro_pvam_1208, retro_pvam_122, retro_pvam_353, retro_pvam_688, retro_pvam_71, retro_pvam_769, retro_pvam_877,
Sus scrofa	ENSSSCG00000016989	3 retrocopies	retro_sscr_1104, retro_sscr_462, retro_sscr_685,
Ictidomys tridecemlineatus	ENSSTOG00000026876	1 retrocopy	retro_itri_1141,
Tarsius syrichta	ENSTSYG00000001655	2 retrocopies	retro_tsyr_1805, retro_tsyr_759,
Tursiops truncatus	ENSTTRG00000010624	8 retrocopies	retro_ttru_1070, retro_ttru_1124, retro_ttru_1694, retro_ttru_1818, retro_ttru_364, retro_ttru_386, retro_ttru_474, retro_ttru_646,