RetrogeneDB ID: retro_lcha_88

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127551.1:722525..722929(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD1
• Ensembl ID: ENSLACG00000014002
• Aliases: None
• Description: None

Sequence

>retro_lcha_88
CCATCCTGATATAGCACTCAGAAGGCAGGGTTCAGTGACACGGAAACCTCACAACCTTTTACCTTCATTTGAAGGAAGTC
CTTTAGTTGAACCCCCCCCCCCCCATCCATACTCTGATGATCAGAGTTACATTGCATTCTCTGTCCAGTTACAAGCCTGT
CCCTTTTAGTGCCTCACTTGGCAGGTCCTTACCAACTAGAGTTGATGAAAGCCATCTTCAAGCACCCATCCAGTTGGCTG
AAGAAGAAAAACCAAAGAGAAAGCCTGTCACATATGAAGAGTTAAGGAACAGGAAAAGAGATGTGTGAAGTGACAGAAAG
GCAGAGATGCTGTTCAAACCTTCCCAAGAAAGAACACCTAAGAAAGAAATTAAAATGAGCCAGTATGGTGGTGCCTGGGA
AGAA

Alignment

ORF - retro_lcha_88 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 52.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPRYGNQKAEFSDTETSQP-LPSFEGSPAIETPL---YSDDYSYIEHS-SSSYEPVPFSASLSESSPTGV
          P..Y..QKA.FSDTETSQP.LPSFEGSP..E......YSDD.SYI..S.SS.Y.PVPFSASL..S.PT.V
Retrocopy PS*YSTQKAGFSDTETSQP>LPSFEGSPLVEXXXXXPYSDDQSYIAFS>SS-YKPVPFSASLGRSLPTRV

Parental  DESYLQAPIQLVEEEKSKRKPVTYEELRNRNRETYEVTMTQKAEILLKPSQERTPKKEVKTNQYGDAWEE
          DES.LQAPIQL.EEEK.KRKPVTYEELRNR.R....V....KAE.L.KPSQERTPKKE.K..QYG.AWEE
Retrocopy DESHLQAPIQLAEEEKPKRKPVTYEELRNRKR---DV*SDRKAEMLFKPSQERTPKKEIKMSQYGGAWEE

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	4.78 RPM
DRP000627_kidney	0.00 RPM	4.02 RPM
DRP000627_pectoral_fin	0.00 RPM	16.36 RPM
DRP000627_pelvic_fin	0.00 RPM	16.57 RPM
DRP000627_pharynx	0.00 RPM	3.45 RPM
DRP000627_tail_muscle	0.00 RPM	3.24 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_88 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011863	1 retrocopy	retro_cpor_928,
Echinops telfairi	ENSETEG00000005961	1 retrocopy	retro_etel_1731,
Latimeria chalumnae	ENSLACG00000014002	1 retrocopy	retro_lcha_88 ,
Macropus eugenii	ENSMEUG00000010655	2 retrocopies	retro_meug_1692, retro_meug_2016,
Monodelphis domestica	ENSMODG00000020640	1 retrocopy	retro_mdom_1103,
Sarcophilus harrisii	ENSSHAG00000018132	1 retrocopy	retro_shar_74,
Ictidomys tridecemlineatus	ENSSTOG00000014963	1 retrocopy	retro_itri_986,