RetrogeneDB ID: retro_lcha_74

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127214.1:75439..75754(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUNDC1
• Ensembl ID: ENSLACG00000010215
• Aliases: None
• Description: None

Sequence

>retro_lcha_74
ATGGCCGCTCGCAGAGCAGACCACGATAGTGATGATGAGTCTTATGAAGTTGTGGATCTGACTGAATATGCAAGACGCCA
CCAGTGGTGGAGTCGTTTGTTTGAACAAAACTCAGGACCAACTGCAGAAAAATATTCTGTGGCTACCCTGATAATGATGG
GTGGATTATCTGAATGGTGTGCAGGATTTTTGTTCCAGAAGACTGGGAAACTTGCAGCTACAGTGGTAGGTGGTGGTTTT
CCTTTGCTACAGATTGCCAATCACAGTCATTATGTACAGGTTTACTGGAAAAGAGTTGAAAGAGATGTAAACCAG

Alignment

ORF - retro_lcha_74 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 69.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASRADRDSDDESYEVVDLTEYARRHQWWSRLFGRNSGPIAEKYSVATQIMMGGISGWCAGFLFQKVGK
          MAA.RAD.DSDDESYEVVDLTEYARRHQWWSRLF..NSGP.AEKYSVAT.IMMGG.S.WCAGFLFQK.GK
Retrocopy MAARRADHDSDDESYEVVDLTEYARRHQWWSRLFEQNSGPTAEKYSVATLIMMGGLSEWCAGFLFQKTGK

Parental  LAATAVGGGFLLLQIANHSGYVQVDWKRVERDVNK
          LAAT.VGGGF.LLQIANHS.YVQV.WKRVERDVN.
Retrocopy LAATVVGGGFPLLQIANHSHYVQVYWKRVERDVNQ

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	0.04 RPM	4.87 RPM
DRP000627_kidney	0.18 RPM	6.31 RPM
DRP000627_pectoral_fin	0.18 RPM	5.30 RPM
DRP000627_pelvic_fin	0.03 RPM	6.39 RPM
DRP000627_pharynx	0.08 RPM	6.59 RPM
DRP000627_tail_muscle	0.19 RPM	5.93 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_74 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 29 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010258	3 retrocopies	retro_amel_586, retro_amel_644, retro_amel_825,
Bos taurus	ENSBTAG00000001637	4 retrocopies	retro_btau_1370, retro_btau_1591, retro_btau_305, retro_btau_587,
Canis familiaris	ENSCAFG00000014506	3 retrocopies	retro_cfam_1269, retro_cfam_1675, retro_cfam_951,
Callithrix jacchus	ENSCJAG00000010876	1 retrocopy	retro_cjac_896,
Cavia porcellus	ENSCPOG00000012962	2 retrocopies	retro_cpor_507, retro_cpor_508,
Dasypus novemcinctus	ENSDNOG00000014551	2 retrocopies	retro_dnov_2091, retro_dnov_2240,
Equus caballus	ENSECAG00000022709	3 retrocopies	retro_ecab_210, retro_ecab_231, retro_ecab_567,
Echinops telfairi	ENSETEG00000012763	3 retrocopies	retro_etel_1614, retro_etel_697, retro_etel_852,
Felis catus	ENSFCAG00000005541	3 retrocopies	retro_fcat_1493, retro_fcat_179, retro_fcat_205,
Homo sapiens	ENSG00000069509	1 retrocopy	retro_hsap_936,
Gorilla gorilla	ENSGGOG00000023311	1 retrocopy	retro_ggor_755,
Latimeria chalumnae	ENSLACG00000010215	1 retrocopy	retro_lcha_74 ,
Macropus eugenii	ENSMEUG00000006795	5 retrocopies	retro_meug_1597, retro_meug_2127, retro_meug_232, retro_meug_415, retro_meug_994,
Microcebus murinus	ENSMICG00000000450	2 retrocopies	retro_mmur_1189, retro_mmur_1461,
Myotis lucifugus	ENSMLUG00000015860	3 retrocopies	retro_mluc_1032, retro_mluc_2302, retro_mluc_2304,
Macaca mulatta	ENSMMUG00000003505	1 retrocopy	retro_mmul_38,
Monodelphis domestica	ENSMODG00000021088	3 retrocopies	retro_mdom_1262, retro_mdom_769, retro_mdom_917,
Mustela putorius furo	ENSMPUG00000012924	1 retrocopy	retro_mputfur_209,
Nomascus leucogenys	ENSNLEG00000002513	2 retrocopies	retro_nleu_2760, retro_nleu_294,
Oryctolagus cuniculus	ENSOCUG00000029753	5 retrocopies	retro_ocun_1008, retro_ocun_1376, retro_ocun_1567, retro_ocun_27, retro_ocun_314,
Pongo abelii	ENSPPYG00000020268	2 retrocopies	retro_pabe_806, retro_pabe_829,
Pelodiscus sinensis	ENSPSIG00000013793	1 retrocopy	retro_psin_30,
Pan troglodytes	ENSPTRG00000021821	1 retrocopy	retro_ptro_648,
Pteropus vampyrus	ENSPVAG00000009327	2 retrocopies	retro_pvam_1380, retro_pvam_232,
Rattus norvegicus	ENSRNOG00000003470	1 retrocopy	retro_rnor_2644,
Sorex araneus	ENSSARG00000012878	4 retrocopies	retro_sara_276, retro_sara_367, retro_sara_494, retro_sara_551,
Sarcophilus harrisii	ENSSHAG00000000501	1 retrocopy	retro_shar_222,
Tarsius syrichta	ENSTSYG00000009139	1 retrocopy	retro_tsyr_1522,
Tursiops truncatus	ENSTTRG00000010466	2 retrocopies	retro_ttru_1099, retro_ttru_1735,