RetrogeneDB ID: retro_lcha_19

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127234.1:101501..102635(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000003922
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACTC1
• Ensembl ID: ENSLACG00000011801
• Aliases: None
• Description: None

Sequence

>retro_lcha_19
ATGTGTGACAATGAAGAAACTACTGCACTGGTCTGCGACAATGGCTCTGGCCTGGTGAAAGCTGGCTTTGCTGGGGATGA
TGCTCCAAGGGCAGTATTTCCATCCATTGTAGGACGCCCACGTCACCAGGGCGTGATGGTAGGCATGGGCCAGAAAGACG
CCTACGTAGGTGATGAGGCACAGAGCAAGAGAGGTATCCTGACACTGAAGTACCCCATCGAACATGGCATTATCACAAAC
TGGGATGACATGGAGAAGATCTGGCACCACACCTTCTACAATGAGCTTCGTGTGGCCCCTGAAGAGCACCCCACTCTGCT
CACAGAGGCACCACTCAATCCCAAGGCCAATCGTGAAAAGATGACCCAAATCATGTTTGAAACCTTCAATGTTCCTGCAA
TGTTTGTTGCTATCCAGGCTGTGCTGTCCCTCTATGCTTCTGGTCGTACCACTGGTATCGTGCTGGACTCTGGAGATGGT
GTCACACACAACGTGCCAATTTATGAAGGTTACGCTCTGCCTCATGCTATCATGCGGTTGGATTTGGCTGGCCGTGACCT
CACTGACTACCTTATGAAGATTCTCACAGAGCGTGGCTACTCCTTTGTCACCACTGCAGAAAGAGAGATTGTCCGTGACA
TTAAAGAGAAACTATGCTATGTTGCACTTGACTTTGAAAATGAGATGGCTACAGCAGCTTCGTCTTCCTCTCTAGAGAAA
AGCTACGAACTTCCTGATGGACAGGTCATCACTATTGGCAATGAGCGTTTCCGCTGCCCTGAAACACTCTTCCAGCCATC
CTTCATTGGAATGGAATCTGCTGGCATCCATGAAACAGCTTACAATAGCATTATGAAGTGCGATATTGACATCAGGAAAG
ACCTTTACGCGAACAACGTCCTGTCTGGTGGCTCCACCATGTACCCCGGTATTGCTGACCGTATGCAAAAGGAAATCACT
GCACTGGCTCCCAGCACCATGAAAATCAAAATCATTGCCCCACCAGAACGCAAGTACTCAGTCTGGATCGGTGGCTCCAT
CCTTGCCTCTCTGTCCACCTTTCAGCAAATGTGGATCACCAAACAAGAATATGATGAGGCTGGCCCATCCATTGTCCATC
GCAAATGTTTCTAA

Alignment

ORF - retro_lcha_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDDEETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK
          MCD.EETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTLK
Retrocopy MCDNEETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDAYVGDEAQSKRGILTLK

Parental  YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQA
          YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAM.VAIQA
Retrocopy YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMFVAIQA

Parental  VLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREI
          VLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREI
Retrocopy VLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREI

Parental  VRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETT
          VRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHET.
Retrocopy VRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETA

Parental  YNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS
          YNSIMKCDIDIRKDLYANNVLSGG.TMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS
Retrocopy YNSIMKCDIDIRKDLYANNVLSGGSTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS

Parental  LSTFQQMWISKQEYDEAGPSIVHRKCF
          LSTFQQMWI.KQEYDEAGPSIVHRKCF
Retrocopy LSTFQQMWITKQEYDEAGPSIVHRKCF

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	10.23 RPM	0.29 RPM
DRP000627_kidney	31.31 RPM	21.00 RPM
DRP000627_pectoral_fin	4.21 RPM	5.20 RPM
DRP000627_pelvic_fin	3.06 RPM	2.64 RPM
DRP000627_pharynx	55.82 RPM	0.02 RPM
DRP000627_tail_muscle	87.36 RPM	0.13 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_19 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000011801	1 retrocopy	retro_lcha_19 ,
Oryctolagus cuniculus	ENSOCUG00000004074	1 retrocopy	retro_ocun_38,
Pongo abelii	ENSPPYG00000006318	1 retrocopy	retro_pabe_1317,