RetrogeneDB ID: retro_lcha_27

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126600.1:1315168..1315713(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSLACG00000009340
• Aliases: None
• Description: ATP synthase subunit beta [Source:UniProtKB/TrEMBL;Acc:H3ALT2]

Sequence

>retro_lcha_27
GTTGCCCTGACTGGTCTAACTGTTGCAAAGTGCTTCCATGAGCAAGGAGGACAGGATGTGTTGCTTTTTATTGTCAACAT
TATCAGATTCACCCAGGTTGGGTCAGAGGTATCTTTCCTTCTGGGTTGTATTCCCTCCATTGTGAGATAGCAGCCAGCAC
TGGCTACTGGTATGGGCACCATGCAGGAAATAATTACAACTACCAAAAAGGGATCCATCACATTAGTACAGGTCATTTTT
GTGTCTGCTGATGACTTGACTGATCCTACTTTTGCTTACTTAGATGCCACAGCTGTTTTGTCCCATGCTAATATAGAAGT
GGGTACACCCAGTTGTGGACCCTTTGGACTCTACTTCCCATATCATAGACCCCCAACATTGTGTGACAAAAGAATTAAGA
TGTGGTCTGTGGTGTGTGGAGGATCTTGCAAGATTAGAAATCACTCCCAGATATTATTGCAGTCTTGGGTGTGAATGAGT
TATCTGAAGGAGACAAGATGACTGTAGCTCATGTTTGTAAAATTCAGCATTTCCTGTCCTGTCCT

Alignment

ORF - retro_lcha_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.62 %
• Parental protein coverage: 59.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKK
          VALTGLTVA..F..Q.GQDVLLFI.NI.RFTQ.GSEVS.LLG.IPS.V..QP.LAT.MGTMQE.ITTTKK
Retrocopy VALTGLTVAKCFHEQGGQDVLLFIVNIIRFTQVGSEVSFLLGCIPSIVR*QPALATGMGTMQEIITTTKK

Parental  GSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDP-LDSTSRILD-PNIVGQEHYD
          GSIT.VQ.I.V.ADDLTDP....TFA.LDAT.VLS.A..E.G..P...P.LDSTS.I.D.PNIV.Q...D
Retrocopy GSITLVQVIFVSADDLTDP----TFAYLDATAVLSHANIEVGT-PSCGP>LDSTSHIID>PNIV*QKN*D

Parental  VARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQP
          V..GV..ILQD.KSL.DIIA.LG..ELSE.DK.TVA...KIQ.FLS.P
Retrocopy VVCGVWRILQD*KSLPDIIAVLGVNELSEGDKMTVAHVCKIQHFLSCP

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	82.22 RPM
DRP000627_kidney	0.00 RPM	101.52 RPM
DRP000627_pectoral_fin	0.00 RPM	116.33 RPM
DRP000627_pelvic_fin	0.00 RPM	166.60 RPM
DRP000627_pharynx	0.00 RPM	104.41 RPM
DRP000627_tail_muscle	0.00 RPM	86.33 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_27 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Latimeria chalumnae	ENSLACG00000009340	1 retrocopy	retro_lcha_27 ,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Xenopus tropicalis	ENSXETG00000024665	1 retrocopy	retro_xtro_68,