RetrogeneDB ID: retro_lcha_14

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: AFYH01279356.1:2500..3289(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000000472
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PLSCR3
• Ensembl ID: ENSLACG00000011730
• Aliases: None
• Description: None

Sequence

>retro_lcha_14
TTTTTTGGGCAGGATTCAAACGGCTCCATGGCTCTGCAAGGCTCTGAAGACAACATTCTTGGTCCACCAGCCTCTGCTTT
CCAGAACCAACCTCAAAATCAAATAACAATTTGGATGCCAGCTCCCCCCATTCCTAGAGACTGTCCACCAGGATTAGAAT
ACCTCACTCAGATAGACCAGATTCTTATTCACCAGCAGGTGTCATTAGTTGAAGCCCTCACTGGCTTTGAAGCAAACAGC
AAATTTGAAATTAAAAACAGCCTGGGGCAGAGAGTCTATTTTGCAGCAGAGGAGAATGACTGCTGTAATCGTAACTTCTG
TGGCGCATTCCGTTCTTTTACTATCAGAGTTCTCGATAATACTGGCCGAGATGTGATGGTGGTATCCAGACCCTTGAGAT
GCAGCACCTGCTGCTTCCCATGCTGCCTCCAGGAGCTGGAGGTTCAGGCTCCTCCAGGGATACCAGTCGGTTACGTTGTC
CAGGAGTGGCATCCTTGCCTGCCTAAGTTCACCATTCAAAACGAAAACAAAGAGGCCGTGCTAAAAATCGTTGGCCCATG
CATTAAATGCAGCTGCTTTAATGATGTTAGCTTTGAGGTGAAATCCGTTGATGAAACAGCAACAGTCGGCAAGATCAGCA
AGCAGTGGACCGGGCTGCTGAAGGAGGCTCTAAGTGCTAGCGACAACTTTGGGATCCAGTTTCCTATGGACCTTGATGTA
AAAATGAAGGCTGTAATGGTTGGTGCTTGCTTCTTAATAGACTTCATGTTTTTTGAACATGGTTCTTAA

Alignment

ORF - retro_lcha_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.17 %
• Parental protein coverage: 79.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGPSPGIGSPDPHGTLT---PYVPIATGVPHGLEYLTQVDQILIHQTVELVEAFIGFETNNKYEIKNSLG
          .GP........P....T...P..PI....P.GLEYLTQ.DQILIHQ.V.LVEA..GFE.N.K.EIKNSLG
Retrocopy LGPPASAFQNQPQNQITIWMPAPPIPRDCPPGLEYLTQIDQILIHQQVSLVEALTGFEANSKFEIKNSLG

Parental  QKIYYAKEENDCCTRNCCGPLRHFNMKITDNTDREVIHLVRPFKCASCWCPCCLQEMEVQSPPGTTIGFI
          Q..Y.A.EENDCC.RN.CG..R.F.....DNT.R.V....RP..C..C..PCCLQE.EVQ.PPG...G..
Retrocopy QRVYFAAEENDCCNRNFCGAFRSFTIRVLDNTGRDVMVVSRPLRCSTCCFPCCLQELEVQAPPGIPVGYV

Parental  IQNWHPFIPKFSIQNVERETVLKVTGSCCMCNCCGDVVFDVKTRDESRSVGRISKQWSGLLKEVFTDTDN
          .Q.WHP..PKF.IQN...E.VLK..G.C..C.C..DV.F.VK..DE...VG.ISKQW.GLLKE.....DN
Retrocopy VQEWHPCLPKFTIQNENKEAVLKIVGPCIKCSCFNDVSFEVKSVDETATVGKISKQWTGLLKEALSASDN

Parental  FGIQFPMDLDVKMKATLMGACFLIDFMFFE
          FGIQFPMDLDVKMKA...GACFLIDFMFFE
Retrocopy FGIQFPMDLDVKMKAVMVGACFLIDFMFFE

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	0.08 RPM	1.07 RPM
DRP000627_kidney	0.00 RPM	0.95 RPM
DRP000627_pectoral_fin	0.08 RPM	1.26 RPM
DRP000627_pelvic_fin	0.79 RPM	5.39 RPM
DRP000627_pharynx	0.01 RPM	0.31 RPM
DRP000627_tail_muscle	0.00 RPM	0.75 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_14 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000011730	1 retrocopy	retro_lcha_14 ,
Mus musculus	ENSMUSG00000019461	1 retrocopy	retro_mmus_1154,