RetrogeneDB ID: retro_lcha_60

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127054.1:1040132..1040735(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAD1L1
• Ensembl ID: ENSLACG00000017346
• Aliases: None
• Description: None

Sequence

>retro_lcha_60
CCCTTTTTATGGAGTAAGTGGCTTAATAAAGGCCTCTATAGGATTGGAGACCTTTATCAAGGCATGATTCTTAAATCATT
TGGTGACCTCCAGAGGGAGTTCTCTCTTGATTCCAGAGAGATTTGGCGGTTCTTCCAACTAAGACATTGCATTTCCCAGT
TTTTCGATGGGAGGGAGAGGGCTCCTGTACTTGGCAAATTTCAGCCTTATTTTGATTCAGCAAGATGTCTACCACATACA
GCAGCACTCATCTACTCCCACCTTATTTCGACCCCTCAGACAGGCTTGAAAGGTCCAATGAGTTATTGGATGAGGGAATG
TAAATTAGAAATGGAAGAGAGAGAATAGGAGAATCACATGAAAAATATGTATCTTCCCCTCCGAGAAGCTAGATTAAAGC
TCCAACAATTTAAAATTATTAATAAGTTATATTGGACTCCCTCACACCTAAGAGCGGTGGGTCTACGAGATAGCAAGAGG
TGTTGGTTTTGTACGGAACAAATAGGCAACCTCCAGCATATGTTATGGAGTTGTAGAAACCTGTCGAGATACTGGGAGGA
AATATTGCAATTTTGTGGTGTGGTGCTTAAAACATCAATTCCC

Alignment

ORF - retro_lcha_60 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.07 %
• Parental protein coverage: 92.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PHLWGNMLPLWCAESLSLLSVKYNCTTLKPFSDLHRQFCLDSKDIWRFFQLRHCIVQLYRDQGKVPLLGE
          P.LW......W....L......Y....LK.F.DL.R.F.LDS..IWRFFQLRHCI.Q........P.LG.
Retrocopy PFLWSK----WLNKGLYRIGDLYQGMILKSFGDLQREFSLDSREIWRFFQLRHCISQFFDGRERAPVLGK

Parental  LLPFYELTRCLPHTAALIYSHLISIPPASMIGPLEYWVRELELELEEGERESLMRNMYLPLREARLKLQH
          ..P.....RCLPHTAALIYSHLIS.P.....GP..YW.RE..LE.EE.E.E..M.NMYLPLREARLKLQ.
Retrocopy FQPYFDSARCLPHTAALIYSHLISTPQTGLKGPMSYWMRECKLEMEERE*ENHMKNMYLPLREARLKLQQ

Parental  FKIVNRLYWTPSHLGVAGLQEGRGCWFCSAQVGDLQHMLWECENLTRFWDEVLQFCGKVLDRPIP
          FKI.N.LYWTPSHL...GL.....CWFC..Q.G.LQHMLW.C.NL.R.W.E.LQFCG.VL...IP
Retrocopy FKIINKLYWTPSHLRAVGLRDSKRCWFCTEQIGNLQHMLWSCRNLSRYWEEILQFCGVVLKTSIP

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	1.12 RPM
DRP000627_kidney	0.00 RPM	0.58 RPM
DRP000627_pectoral_fin	0.00 RPM	3.42 RPM
DRP000627_pelvic_fin	0.00 RPM	3.94 RPM
DRP000627_pharynx	0.00 RPM	0.51 RPM
DRP000627_tail_muscle	0.00 RPM	0.43 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_60 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000014242	1 retrocopy	retro_ecab_724,
Latimeria chalumnae	ENSLACG00000017346	17 retrocopies	retro_lcha_102, retro_lcha_106, retro_lcha_109, retro_lcha_113, retro_lcha_114, retro_lcha_115, retro_lcha_33, retro_lcha_36, retro_lcha_41, retro_lcha_44, retro_lcha_60 , retro_lcha_66, retro_lcha_70, retro_lcha_79, retro_lcha_80, retro_lcha_93, retro_lcha_99,