RetrogeneDB ID: retro_lcha_97

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127969.1:94176..94733(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000010217
• Aliases: None
• Description: None

Sequence

>retro_lcha_97
ATCTTGGAGAGACACATAGAGTTCAACGAACCCCTGTTCTGCACATTCGTTGACTTTAAGAAAGCATTCAACTCCATTAA
CAGAGAGGATCTGTGGAAAGTACTCAAGTGGTATGGTTTTAGCAGCAAGCTGATTCAAATACTGCAGAGTCTGTATAGCA
TAGCTTGGCGTGCAGTAAGAGTCAAGGGCGAGCTGACAAAGTGGCTTGAAGTGAAAACTGGAGTTAAACAAGGATGCATA
CTCAGTCCAGTACTTTTTGCTCTATACTTAGAAAACATCTTGTCCAACTCCCTTAGTAACAATGGTGGAGGCTGCATGAT
ATTGGGACAAATTATCAATCACCTTGATTTTGCAGACAATATCGTAATGAGAAGGAAATGAGAATACAACCAAGAAGCAG
CAAATAACTTGTACACAACAGCCAGAGAATGGGGATTAAAAATAAACAAAAGACCAAACTAGTGGTAACATCAAAAATCA
AGAAGCAGGCTAAACTAGTCATTAACAGTGTAAACATCAAACAAGTAGGCAGCTTCTGCTACTTGGGTTCCATCATA

Alignment

ORF - retro_lcha_97 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.35 %
• Parental protein coverage: 94.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IVLNHIDVSLLSKLSFIDFIIKKSYLSIDREALWKVLKWYGFSSKLIQILQSLYSIAWHAVRVNGELTEW
          I...HI.........F.DF..KK...SI.RE.LWKVLKWYGFSSKLIQILQSLYSIAW.AVRV.GELT.W
Retrocopy ILERHIEFNEPLFCTFVDF--KKAFNSINREDLWKVLKWYGFSSKLIQILQSLYSIAWRAVRVKGELTKW

Parental  FEVKNGVEQGCILSPILFALYLENILSNSLSNIGGGCMISGQIINHLDFADDIVMIMPMEECNQEAANNL
          .EVK.GV.QGCILSP.LFALYLENILSNSLSN.GGGCMI.GQIINHLDFAD.IV......E.NQEAANNL
Retrocopy LEVKTGVKQGCILSPVLFALYLENILSNSLSNNGGGCMILGQIINHLDFADNIV-MRRK*EYNQEAANNL

Parental  YTTARKW-GLKMNEQKTKLMVTSKIKKQAKLVINGGNTEQVDSFCYLGPII
          YTTAR.W.G.K.N.QKTKL.VTSKIKKQAKLVIN..N..QV.SFCYLG.II
Retrocopy YTTAREW<GIK-NKQKTKLVVTSKIKKQAKLVINSVNIKQVGSFCYLGSII

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	0.00 RPM
DRP000627_pectoral_fin	0.00 RPM	0.00 RPM
DRP000627_pelvic_fin	0.00 RPM	0.00 RPM
DRP000627_pharynx	0.00 RPM	0.00 RPM
DRP000627_tail_muscle	0.00 RPM	0.00 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_97 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	ENSLACG00000010217	1 retrocopy	retro_lcha_97 ,