RetrogeneDB ID: retro_lcha_25

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126584.1:431092..431335(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHF5A
• Ensembl ID: ENSLACG00000012094
• Aliases: None
• Description: None

Sequence

>retro_lcha_25
ATGGTGAAGCATCACCCTGAGCTCATCTTCTGCAGGAAGCAAGCCGGCGTGGCTATCAGAAGGCTGTGTGAAAAATGTGA
TGGTAAATGCATGATCTGCGATTCCTACGTGAGGCCGTGCATGCTGGTGTGAATCTGCGATGAGTGTAATTATGGGTCCT
ACCAAGGCCGCTGCGTAATCTGCGGAGGGCCTGGTGTCTCGGATGCTTACTATTGTAAAGAATGCACGATTCAGGAAAAA
GAT

Alignment

ORF - retro_lcha_25 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.59 %
• Parental protein coverage: 87.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAY
          M.KHHP.LIFCRKQAGVAI.RLCEKCDGKC.ICDSYVRPC.LV.ICDECNYGSYQGRCVICGGPGVSDAY
Retrocopy MVKHHPELIFCRKQAGVAIRRLCEKCDGKCMICDSYVRPCMLV*ICDECNYGSYQGRCVICGGPGVSDAY

Parental  YCKECTIQEKD
          YCKECTIQEKD
Retrocopy YCKECTIQEKD

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	5.10 RPM	4.52 RPM
DRP000627_kidney	6.85 RPM	4.46 RPM
DRP000627_pectoral_fin	7.73 RPM	6.56 RPM
DRP000627_pelvic_fin	9.91 RPM	11.80 RPM
DRP000627_pharynx	4.51 RPM	3.48 RPM
DRP000627_tail_muscle	2.62 RPM	2.37 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_25 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.

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015687	1 retrocopy	retro_amel_1674,
Canis familiaris	ENSCAFG00000001090	1 retrocopy	retro_cfam_369,
Callithrix jacchus	ENSCJAG00000004999	3 retrocopies	retro_cjac_1194, retro_cjac_1527, retro_cjac_906,
Echinops telfairi	ENSETEG00000010741	1 retrocopy	retro_etel_102,
Homo sapiens	ENSG00000100410	3 retrocopies	retro_hsap_2033, retro_hsap_2647, retro_hsap_2829,
Gorilla gorilla	ENSGGOG00000001104	2 retrocopies	retro_ggor_1848, retro_ggor_1965,
Latimeria chalumnae	ENSLACG00000012094	1 retrocopy	retro_lcha_25 ,
Microcebus murinus	ENSMICG00000013520	1 retrocopy	retro_mmur_758,
Macaca mulatta	ENSMMUG00000011354	3 retrocopies	retro_mmul_1390, retro_mmul_1471, retro_mmul_1503,
Mustela putorius furo	ENSMPUG00000016398	2 retrocopies	retro_mputfur_359, retro_mputfur_439,
Mus musculus	ENSMUSG00000061360	3 retrocopies	retro_mmus_1070, retro_mmus_1071, retro_mmus_1155,
Nomascus leucogenys	ENSNLEG00000015481	2 retrocopies	retro_nleu_1205, retro_nleu_653,
Oryctolagus cuniculus	ENSOCUG00000012705	1 retrocopy	retro_ocun_640,
Otolemur garnettii	ENSOGAG00000002839	1 retrocopy	retro_ogar_55,
Pongo abelii	ENSPPYG00000011870	2 retrocopies	retro_pabe_1661, retro_pabe_2324,
Pan troglodytes	ENSPTRG00000014427	3 retrocopies	retro_ptro_1352, retro_ptro_1917, retro_ptro_2479,
Pteropus vampyrus	ENSPVAG00000001162	1 retrocopy	retro_pvam_66,
Rattus norvegicus	ENSRNOG00000024170	3 retrocopies	retro_rnor_2660, retro_rnor_2704, retro_rnor_2712,
Tarsius syrichta	ENSTSYG00000001082	1 retrocopy	retro_tsyr_259,
Tursiops truncatus	ENSTTRG00000003369	1 retrocopy	retro_ttru_1483,