RetrogeneDB ID: retro_lcha_64

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127146.1:574929..575232(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM14A
• Ensembl ID: ENSLACG00000012581
• Aliases: None
• Description: None

Sequence

>retro_lcha_64
ATGCCTCTTGATTGGATTGGTTTTAGCTATGCAGCTTTGGTTGCTTCAGGAGGAGTTGTTGGCTATGTGAAAAAAGGCAG
TGTCCCTTCCTTGGTTGCTGGCCTTGTGTTTGGGAGTGTAGCAGGACTGGGTGCTTATCAGACCTCTCAAGATCCCAAGA
ATGTCTGGCTGTCTCTGTTGGCATGTGGGACTTTGACTGGAGTCATGGGGTATAGGTTTTATAACTCGGGAAAATTCATG
CCAGCCGGCTTAGTTGCAACTGCAAGTCTGCTGATGCTGGGAAGACTTGGAATGAGGATGATG

Alignment

ORF - retro_lcha_64 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPVDWIGFGYAAAITLGGVLGYKKKGSVMSLIAGLVFGSLSGYGAYAVSNDPKDVKLSLFAAFTLTTIMG
          MP.DWIGF.YAA....GGV.GY.KKGSV.SL.AGLVFGS..G.GAY..S.DPK.V.LSL.A..TLT..MG
Retrocopy MPLDWIGFSYAALVASGGVVGYVKKGSVPSLVAGLVFGSVAGLGAYQTSQDPKNVWLSLLACGTLTGVMG

Parental  VRYRRSKKFMPAGLIAFLSLLMVLRLGFMLL
          .R...S.KFMPAGL.A..SLLM..RLG....
Retrocopy YRFYNSGKFMPAGLVATASLLMLGRLGMRMM

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	15.42 RPM	7.60 RPM
DRP000627_kidney	16.73 RPM	4.59 RPM
DRP000627_pectoral_fin	30.90 RPM	15.95 RPM
DRP000627_pelvic_fin	29.27 RPM	20.10 RPM
DRP000627_pharynx	15.20 RPM	2.65 RPM
DRP000627_tail_muscle	11.39 RPM	1.98 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_64 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005206	1 retrocopy	retro_btau_505,
Latimeria chalumnae	ENSLACG00000012581	1 retrocopy	retro_lcha_64 ,
Microcebus murinus	ENSMICG00000016339	1 retrocopy	retro_mmur_211,
Mustela putorius furo	ENSMPUG00000008935	2 retrocopies	retro_mputfur_157, retro_mputfur_586,
Sorex araneus	ENSSARG00000005516	1 retrocopy	retro_sara_307,
Tupaia belangeri	ENSTBEG00000011162	1 retrocopy	retro_tbel_1562,
Tarsius syrichta	ENSTSYG00000004269	1 retrocopy	retro_tsyr_1783,
Tursiops truncatus	ENSTTRG00000015237	1 retrocopy	retro_ttru_1442,
Vicugna pacos	ENSVPAG00000004486	1 retrocopy	retro_vpac_450,