RetrogeneDB ID: retro_lcha_112

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH128783.1:169244..169589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB4
• Ensembl ID: ENSLACG00000015430
• Aliases: None
• Description: None

Sequence

>retro_lcha_112
CAACATCTAAGACAGTTTTGCCTTGAACTCAATGGACTTGCTGTCAAGCTGCGGAGTGAATGTCACCCTGACACACGTAC
TCAGATGACTGCATCTGAACAACGGATTTTTCTGTATGCTGTTCACAAAACTCCAAAAGAGTGCCCTGCAATAGACTATA
CCAGACACACATTGGATGGTGCAGCCTGCCTTCTGAACAGTAATAAATATTTCCCCAGCATGGTTAGCATTAAAGACTCC
TCTGTAGCTAAACTTGGATTAGTGTGCCGTAGGATTTACCGAATATTTTCACATGCCTATTTTCATCATCGACAAATATT
CGATGAATATGAGAATTATAACTTT

Alignment

ORF - retro_lcha_112 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.43 %
• Parental protein coverage: 51.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EHLRQFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKY
          .HLRQFCLELNGLAVKL.SECHPDT.TQMTA.EQ.IFL.A.HKTPKECPAIDYTRHTLDGAACLLNSNKY
Retrocopy QHLRQFCLELNGLAVKLRSECHPDTRTQMTASEQRIFLYAVHKTPKECPAIDYTRHTLDGAACLLNSNKY

Parental  FPSRVSIKDSSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETF
          FPS.VSIKDSSVAKLG.VCRRIYRIFSHAYFHHRQIFDEYEN..F
Retrocopy FPSMVSIKDSSVAKLGLVCRRIYRIFSHAYFHHRQIFDEYENYNF

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	0.00 RPM	11.58 RPM
DRP000627_kidney	0.00 RPM	9.04 RPM
DRP000627_pectoral_fin	0.00 RPM	10.26 RPM
DRP000627_pelvic_fin	0.00 RPM	13.43 RPM
DRP000627_pharynx	0.02 RPM	18.50 RPM
DRP000627_tail_muscle	0.02 RPM	14.46 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_112 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 21 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000884	5 retrocopies	retro_chof_1077, retro_chof_1354, retro_chof_1631, retro_chof_177, retro_chof_213,
Callithrix jacchus	ENSCJAG00000004020	2 retrocopies	retro_cjac_1960, retro_cjac_3238,
Cavia porcellus	ENSCPOG00000012746	2 retrocopies	retro_cpor_318, retro_cpor_804,
Dasypus novemcinctus	ENSDNOG00000008252	1 retrocopy	retro_dnov_211,
Echinops telfairi	ENSETEG00000000932	1 retrocopy	retro_etel_952,
Homo sapiens	ENSG00000115540	2 retrocopies	retro_hsap_2275, retro_hsap_906,
Gorilla gorilla	ENSGGOG00000009005	2 retrocopies	retro_ggor_733, retro_ggor_743,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112 ,
Microcebus murinus	ENSMICG00000008599	1 retrocopy	retro_mmur_1280,
Macaca mulatta	ENSMMUG00000016547	1 retrocopy	retro_mmul_829,
Monodelphis domestica	ENSMODG00000012305	2 retrocopies	retro_mdom_1333, retro_mdom_963,
Nomascus leucogenys	ENSNLEG00000006881	2 retrocopies	retro_nleu_287, retro_nleu_376,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,
Otolemur garnettii	ENSOGAG00000000272	1 retrocopy	retro_ogar_2739,
Ochotona princeps	ENSOPRG00000016650	2 retrocopies	retro_opri_444, retro_opri_812,
Pongo abelii	ENSPPYG00000013047	6 retrocopies	retro_pabe_1943, retro_pabe_2021, retro_pabe_3600, retro_pabe_781, retro_pabe_795, retro_pabe_970,
Pan troglodytes	ENSPTRG00000012775	3 retrocopies	retro_ptro_1609, retro_ptro_626, retro_ptro_640,
Sarcophilus harrisii	ENSSHAG00000017821	1 retrocopy	retro_shar_351,
Sus scrofa	ENSSSCG00000016079	2 retrocopies	retro_sscr_804, retro_sscr_824,
Ictidomys tridecemlineatus	ENSSTOG00000021024	1 retrocopy	retro_itri_727,
Tarsius syrichta	ENSTSYG00000001726	1 retrocopy	retro_tsyr_1673,