RetrogeneDB ID: retro_lcha_1

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126821.1:1664417..1665029(+)
• Located in intron of: ENSLACG00000016299

Retrocopy information

• Ensembl ID: ENSLACG00000016644
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: mibp2 (2 of 2)
• Ensembl ID: ENSLACG00000002210
• Aliases: None
• Description: muscle-specific beta 1 integrin binding protein 2 [Source:ZFIN;Acc:ZDB-GENE-031113-14]

Sequence

>retro_lcha_1
ATGAAGTACATAATCGGTATCGGCGGTGTCACTAATGGTGGAAAAACAACTCTTACAAACCAGTTGATTAAAATGCTGCC
TAATTGTTGTGTTGTACATCAAGATGACTTCTTTAAGCCCCAAGATCAAATAGAAGTTGGTGAAGATGGATTCAAGCAGT
ATGATGTGATTACAGCATTGGATATGGAGGCAATGATTAACACCATCTATGGCTGGATTGAAAATCCAGTGAAGTTTGAA
CGCTCACATGGCATTAACACCCTTGATGCTGAGATTACACCAGACTCCAAAGATAAGGATGAAGGCCTTCACATTCTTAT
TGTGGAGGGCTTTCTTCTCTATACTTATAAGCCCCTTATCAATATTTTCAACAAACGTTACTTTCTCTCCGTTCCATATG
AAGAGTGCAAAAGGAGGAGGAGTTCAAGGAACTATACTGTGCCTGATCCACCTGGTCTGTTTGATGGTCATGTTTGGCCA
ATGTATGTGAAACACACAAAGATAATGGAGGACATGAATGTTGATGTTTGTCATTTGGATGGAACCAAGTCCAAGGTAGG
CTTGTTTAATGAGGTTTATGGAGAAATACAGAATGAAATTGAAAACCTAAAG

Alignment

ORF - retro_lcha_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKYIIGIGGVTNGGKTTLTNQLIKMLPNCCVVHQDDFFKPQDQIEVGEDGFKQYDVITALDMEAMINTIY
          MKYIIGIGGVTNGGKTTLTNQLIKMLPNCCVVHQDDFFKPQDQIEVGEDGFKQYDVITALDMEAMINTIY
Retrocopy MKYIIGIGGVTNGGKTTLTNQLIKMLPNCCVVHQDDFFKPQDQIEVGEDGFKQYDVITALDMEAMINTIY

Parental  GWIENPVKFERSHGINTLDAEITPDSKDKDEGLHILIVEGFLLYTYRPLINIFNKCYFLSVPYEECKRRR
          GWIENPVKFERSHGINTLDAEITPDSKDKDEGLHILIVEGFLLYTY.PLINIFNK.YFLSVPYEECKRRR
Retrocopy GWIENPVKFERSHGINTLDAEITPDSKDKDEGLHILIVEGFLLYTYKPLINIFNKRYFLSVPYEECKRRR

Parental  KSSRNYTVPDPPGLFDGHVWPMYVKHTKIMEDMNVDVCHLDGTKSKVGLFNEVYEEIQNEIENLK
          .SSRNYTVPDPPGLFDGHVWPMYVKHTKIMEDMNVDVCHLDGTKSKVGLFNEVY.EIQNEIENLK
Retrocopy -SSRNYTVPDPPGLFDGHVWPMYVKHTKIMEDMNVDVCHLDGTKSKVGLFNEVYGEIQNEIENLK

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	2.00 RPM	15.65 RPM
DRP000627_kidney	2.38 RPM	16.19 RPM
DRP000627_pectoral_fin	0.85 RPM	8.22 RPM
DRP000627_pelvic_fin	1.14 RPM	8.92 RPM
DRP000627_pharynx	2.97 RPM	26.16 RPM
DRP000627_tail_muscle	2.13 RPM	21.98 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_1 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000002210	1 retrocopy	retro_lcha_1 ,