RetrogeneDB ID: retro_lcha_23

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126569.1:1196502..1196949(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000015191
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CFL2
• Ensembl ID: ENSLACG00000018011
• Aliases: None
• Description: None

Sequence

>retro_lcha_23
ATGAAAGTAAGGAAGTCCTCAACACAGGAGGAAGTCAAAAAGAGAAAGAAAGCAGTACTTTTTTGCCTCAGTGATGACAA
GCGTTATATCATTGTCGAGGAAGGAAAGGAGATCTTGGTGGGTGACATTGGAGTGAGTGTAGAGGACCCCTATGGAGCCT
TTGTAGATCTGCTACCTGCAGCTGATTGCCGATATGCTTTATATGATGCTACATATGAAACAAGAGAGTCTAAGAAAGAA
GACTTGGTGTTTATATTCTGGGCCCCAGAGAATGCACCTCTAAAAAGTAAGATGATTTATGCTAGCTCTAAAGATGCCAT
TAAAAAGAAATTTACAGGCATTAAACATGAATGGCAAGTCAATGGCTTAGAGGATATTAATCACATTTCAACACTTGCAG
AAAAGCTGGGAGGCAATGCGATAGTTTCACTTGAAGGAAAACCTTTG

Alignment

ORF - retro_lcha_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKVRKSSTQEEVKKRKKAVLFCLSDDKRYIIVEEGKEILVGDIGVSVEDPYGAFVDLLPAADCRYALYDA
          MKVRKSSTQEEVKKRKKAVLFCLSDDKRYIIVEEGKEILVGDIGVSVEDPYGAFVDLLPAADCRYALYDA
Retrocopy MKVRKSSTQEEVKKRKKAVLFCLSDDKRYIIVEEGKEILVGDIGVSVEDPYGAFVDLLPAADCRYALYDA

Parental  TYETRESKKEDLVFIFWAPENAPLKSKMIYASSKDAIKKKFTGIKHEWQVNGLEDIKHISTLAEKLGGNA
          TYETRESKKEDLVFIFWAPENAPLKSKMIYASSKDAIKKKFTGIKHEWQVNGLEDI.HISTLAEKLGGNA
Retrocopy TYETRESKKEDLVFIFWAPENAPLKSKMIYASSKDAIKKKFTGIKHEWQVNGLEDINHISTLAEKLGGNA

Parental  IVSLEGKPL
          IVSLEGKPL
Retrocopy IVSLEGKPL

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	0.69 RPM	40.49 RPM
DRP000627_kidney	1.20 RPM	50.97 RPM
DRP000627_pectoral_fin	0.59 RPM	16.78 RPM
DRP000627_pelvic_fin	1.53 RPM	28.79 RPM
DRP000627_pharynx	2.10 RPM	70.18 RPM
DRP000627_tail_muscle	1.71 RPM	54.56 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_23 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 22 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015508	1 retrocopy	retro_amel_1347,
Canis familiaris	ENSCAFG00000032562	1 retrocopy	retro_cfam_1006,
Cavia porcellus	ENSCPOG00000008996	1 retrocopy	retro_cpor_1003,
Dasypus novemcinctus	ENSDNOG00000017048	7 retrocopies	retro_dnov_1072, retro_dnov_1379, retro_dnov_1697, retro_dnov_2195, retro_dnov_2691, retro_dnov_715, retro_dnov_905,
Erinaceus europaeus	ENSEEUG00000013155	4 retrocopies	retro_eeur_335, retro_eeur_448, retro_eeur_513, retro_eeur_578,
Echinops telfairi	ENSETEG00000006010	3 retrocopies	retro_etel_1579, retro_etel_1622, retro_etel_684,
Felis catus	ENSFCAG00000008480	2 retrocopies	retro_fcat_1223, retro_fcat_1395,
Latimeria chalumnae	ENSLACG00000018011	1 retrocopy	retro_lcha_23 ,
Loxodonta africana	ENSLAFG00000010579	1 retrocopy	retro_lafr_1041,
Macropus eugenii	ENSMEUG00000000739	11 retrocopies	retro_meug_1026, retro_meug_1138, retro_meug_125, retro_meug_1266, retro_meug_1666, retro_meug_1791, retro_meug_2025, retro_meug_2062, retro_meug_210, retro_meug_321, retro_meug_668,
Microcebus murinus	ENSMICG00000009237	1 retrocopy	retro_mmur_493,
Monodelphis domestica	ENSMODG00000012949	1 retrocopy	retro_mdom_171,
Mus musculus	ENSMUSG00000062929	1 retrocopy	retro_mmus_660,
Oryctolagus cuniculus	ENSOCUG00000009383	1 retrocopy	retro_ocun_1397,
Otolemur garnettii	ENSOGAG00000032321	1 retrocopy	retro_ogar_2346,
Pteropus vampyrus	ENSPVAG00000002798	1 retrocopy	retro_pvam_398,
Rattus norvegicus	ENSRNOG00000045892	1 retrocopy	retro_rnor_684,
Sarcophilus harrisii	ENSSHAG00000004732	1 retrocopy	retro_shar_528,
Sus scrofa	ENSSSCG00000001959	2 retrocopies	retro_sscr_1198, retro_sscr_327,
Ictidomys tridecemlineatus	ENSSTOG00000001675	3 retrocopies	retro_itri_1313, retro_itri_581, retro_itri_632,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,
Vicugna pacos	ENSVPAG00000003273	1 retrocopy	retro_vpac_644,