RetrogeneDB ID: retro_lcha_107

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH128386.1:288743..289214(+)
• Located in intron of: ENSLACG00000007555

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000002156
• Aliases: None
• Description: None

Sequence

>retro_lcha_107
AGTAAACAGCCGTTTACTTCTTCCCCTCGTTCCAGCAGCCCACCTCCCAGCTTCCCAGCAGGACCCTTGGAAGATCTGGC
CACCGACATTAAAAGGATTTTTCTTGTCTTTATTAAACTATCTACTGATTTTGAAGCTTTTAAATCTAATCTACAGTCAC
TCCAATCCTCGGTAAATAGTCTGGGAACAAAGATAACAGCTGCAGACACAAGAATTTCGTCAATAGAAGATGAGAATTGG
TCGAGGGACAACCTGTCTCAACAGCTGCAAACACAGCTTACGACGGCAGTGGCTCGGATTGACGACCTTGAAAACCGCTC
CCACCACAACAATATTAGAATCCTAGGATTCCCTGAGGGGGTAGAAGGGGGCAACCCCTCTTCCTTCTTAGCTTGAGTGA
TACCTAAACTGCTGGACCTGGACCCTTCTACACCTCTGGACATTGAGCAGGTTCATCACTCCCTGACCCCC

Alignment

ORF - retro_lcha_107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.51 %
• Parental protein coverage: 59.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TNQSITSALTLSNSLWSFHDEQVSRKRSHIKKIFLVLHKLSTDFEGFKNDLQSIEASVNNLGSKITAAET
          ..Q..TS....S....SF...........IK.IFLV..KLSTDFE.FK..LQS...SVN.LG.KITAA.T
Retrocopy SKQPFTSSPRSSSPPPSFPAGPLEDLATDIKRIFLVFIKLSTDFEAFKSNLQSLQSSVNSLGTKITAADT

Parental  RISQIEDENKSRDTQSQLLHSQLVAAVARIDDLENRSRRNNIRILVFPEGIEGNNPSSFLSKTLPDLLGL
          RIS.IEDEN.SRD..SQ.L..QL..AVARIDDLENRS..NNIRIL.FPEG.EG.NPSSFL....P.LL.L
Retrocopy RISSIEDENWSRDNLSQQLQTQLTTAVARIDDLENRSHHNNIRILGFPEGVEGGNPSSFLA*VIPKLLDL

Parental  DSSEPLEIERAHRSLGP
          D.S.PL.IE..H.SL.P
Retrocopy DPSTPLDIEQVHHSLTP

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	0.01 RPM	0.02 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_107 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	ENSLACG00000000522	1 retrocopy	retro_lcha_126,
Latimeria chalumnae	ENSLACG00000002156	1 retrocopy	retro_lcha_107 ,