RetrogeneDB ID: retro_lcha_122

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH129974.1:78874..79321(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000000639
• Aliases: None
• Description: None

Sequence

>retro_lcha_122
TTTTACTTTAATTTGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCAGCTGCATTTTCATCTCCGCTCATTGGACTGTA
TGGCAGTGATGTCATCCTGAGGTGCATGTTCCCTCATGGGCACGGCAACGATGCTCCGGAACTGATCATTATCTGGCAGA
AGAAAAACCCCAGTGGTCCGGATGACGTTGTTCACAGTTACTATTACCAGCGGGATCAGCTGGATCGGCAGCATGAGGCT
TACAGAAACCGGACACGGATATTCCCGGAAGAATTCCCCAAGGAAAACGCTTCCCTAAAGCTGATCAGAGTCCATCCTGG
GGATGAGGGCAGTTATCTTTGTTATGTTGAGAACAAGAAGATTGTCCAGTGCACTGTGGAGCTTGTAGTGGCAGGTAAGA
GCCAAATGCAGTATTGCCTGTTTCAATGTCACACAAGGAAGGGGTTT

Alignment

ORF - retro_lcha_122 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.33 %
• Parental protein coverage: 52.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FYSAIKRICVLLLSFSSVVSSPLVALYGSDVILSCTFPHGHSSDTREPIIIWQKKKSSGLDDVVHSYYYQ
          FY.................SSPL..LYGSDVIL.C.FPHGH..D..E.IIIWQKK..SG.DDVVHSYYYQ
Retrocopy FYFNLXXXXXXXXXXAAAFSSPLIGLYGSDVILRCMFPHGHGNDAPELIIIWQKKNPSGPDDVVHSYYYQ

Parental  QDQLDLQDEAYRNQTQMFPEEFHKGNASLKLMRVRLTDEGTYLCYVENKEVSGQYCRDVVVAAPYTEPNL
          .DQLD.Q.EAYRN.T..FPEEF.K.NASLKL.RV...DEG.YLCYVENK....Q.....VVA........
Retrocopy RDQLDRQHEAYRNRTRIFPEEFPKENASLKLIRVHPGDEGSYLCYVENKKIV-QCTVELVVAGKSQMQYC

Parental  TFDLSNQDGY
          .F......G.
Retrocopy LFQCHTRKGF

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	0.00 RPM
DRP000627_kidney	0.00 RPM	0.04 RPM
DRP000627_pectoral_fin	0.00 RPM	0.04 RPM
DRP000627_pelvic_fin	0.00 RPM	0.86 RPM
DRP000627_pharynx	0.00 RPM	0.03 RPM
DRP000627_tail_muscle	0.00 RPM	0.06 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_122 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	ENSLACG00000000639	1 retrocopy	retro_lcha_122 ,
Ictidomys tridecemlineatus	ENSSTOG00000021193	1 retrocopy	retro_itri_371,