RetrogeneDB ID: retro_lcha_98

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127993.1:123572..124007(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000013075
• Aliases: None
• Description: None

Sequence

>retro_lcha_98
CTTCTTATGCAAAACCCTGTCCAATCTATTCTGGTACTGTTAGGTATTTTAACTTTGTTTGGCCCTATATCAGGATTTAA
GGTAAATTGGTCCAAATCGGAGGTAATGCATCTAAGCGTTCACTGTACCTCATGAGAATTACATGAGTTTCCCTTTATTA
TCAAACAGCAATATATGAAATATCTAGGAATTATGTTTACTTCCTCTTTCAAAAACTTATTCCAAGAAAATGGGCCCCGA
ATATTTAAAGTGATTAAGGAGGACTTGGACAGATGGTAACATCTTCCGCTCGCCCTGTGGGGTAAGGTGGATATCCTAAA
GATGAACATTTTGCCTCGACTTCTATACGTGGTGGCCTCTGTCCCCATGCAATTCCCCTGTTCATGGTTCCGGAAGATTA
AAAACGCCTTCTTAAAATTTGTTTGGGGTACTAAG

Alignment

ORF - retro_lcha_98 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.68 %
• Parental protein coverage: 61.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLTLTQSESIPVFMRIIDQYHILAIFKINWNKSEILPLNIQCN---ISKFPFE-KKHYLKYLGIRLSSSF
          LL......SI.V...I.........FK.NW.KSE...L...C.......FPF..K..Y.KYLGI...SSF
Retrocopy LLMQNPVQSILVLLGILTLFGPISGFKVNWSKSEVMHLSVHCTS*ELHEFPFIIKQQYMKYLGIMFTSSF

Parental  KELFKENGPTILKEIKEDLDRRHNLPLII----DTIKMNILFRLLYVVTSVPVGFPSQWFQQVRTAFIKF
          K.LF.ENGP.I.K.IKEDLDR...LPL......D..KMNIL.RLLYVV.SVP..FP..WF.....AF.KF
Retrocopy KNLFQENGPRIFKVIKEDLDRW*HLPLALWGKVDILKMNILPRLLYVVASVPMQFPCSWFRKIKNAFLKF

Parental  IWRGTK
          .W.GTK
Retrocopy VW-GTK

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	0.01 RPM	0.07 RPM
DRP000627_kidney	0.00 RPM	0.14 RPM
DRP000627_pectoral_fin	0.00 RPM	0.00 RPM
DRP000627_pelvic_fin	0.00 RPM	0.00 RPM
DRP000627_pharynx	0.00 RPM	0.09 RPM
DRP000627_tail_muscle	0.00 RPM	0.02 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_98 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 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000013075	4 retrocopies	retro_lcha_105, retro_lcha_116, retro_lcha_125, retro_lcha_98 ,