RetrogeneDB ID: retro_lcha_22

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126562.1:6131472..6131718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHIC2
• Ensembl ID: ENSLACG00000006603
• Aliases: None
• Description: None

Sequence

>retro_lcha_22
CTGTTTGGACTTAGCAACAAGTTTAAATCTGAGTTTCCATCGTCGCTAACAGGAAAGGTTGCACCTGAAGAGTTCAAAGC
TAGTATTAATCGAGTTAATAGCTGTCCGAAGAAGACTCTTCCAGTCAAGGTACGGTGGTTCCTTTGTGGCTACTTCTGTT
GTTGTACTTTGGGCTGCAGTATGTGGCCGGTCATTTGTCTCAGTAAGAGAACATGAAGATCGATCGAGAAGTTATTCGAA
TGAGAA

Alignment

ORF - retro_lcha_22 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.54 %
• Parental protein coverage: 50.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFGLSNKFESEFPSSLTGKVAPEEFKASINRVNSCLKKNLPVNVRWLLCGCLCCCCTLGCSMWPVICLSK
          .FGLSNKF.SEFPSSLTGKVAPEEFKASINRVNSC.KK.LPV.VRW.LCG...CCCTLGCSMWPVICLSK
Retrocopy LFGLSNKFKSEFPSSLTGKVAPEEFKASINRVNSCPKKTLPVKVRWFLCGYF-CCCTLGCSMWPVICLSK

Parental  RTRRSIEKLLEWE
          RT.RSIEKL.E.E
Retrocopy RT*RSIEKLFE*E

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	0.32 RPM
DRP000627_kidney	0.00 RPM	0.35 RPM
DRP000627_pectoral_fin	0.00 RPM	1.03 RPM
DRP000627_pelvic_fin	0.00 RPM	0.65 RPM
DRP000627_pharynx	0.00 RPM	0.41 RPM
DRP000627_tail_muscle	0.00 RPM	0.43 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_22 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024493	1 retrocopy	retro_cpor_1448,
Echinops telfairi	ENSETEG00000004296	1 retrocopy	retro_etel_1804,
Latimeria chalumnae	ENSLACG00000006603	1 retrocopy	retro_lcha_22 ,
Loxodonta africana	ENSLAFG00000012248	1 retrocopy	retro_lafr_953,
Macaca mulatta	ENSMMUG00000006382	1 retrocopy	retro_mmul_1372,