RetrogeneDB ID: retro_lcha_67

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127173.1:225982..226894(-)
• Located in intron of: ENSLACG00000006579

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAK16
• Ensembl ID: ENSLACG00000018758
• Aliases: None
• Description: None

Sequence

>retro_lcha_67
ATGCAGCACGACGATGTGATATGGGACATTATAGGAAACAAACAGTTTTGTTCCTTTAAAGTGAGAACAAAGACTCAAAG
CTTCTGCCGGAATGAGTATAACATTACAGGCCTGTGTAACCGTTCATCATGTCCCCTTGCCAACAGTCAGTATGCAACTG
TCAGAGAGGAGAAAGGCCAGTGTTACCTGTATATGAAGATGATAGAAAGGGCAGCATTTCCAGCCCGCTTGTGGGAAAGG
GTAAAGCTAAGTAAGAATTATGAAAAGGCGTTGGAACAGATTGATGAAAACCTAATTTACTGGCCACGCTTCATCAGACA
TAAATGCAAACAGCGGTTTACCAAAATCACACAGTATCTTATCAGAATAAGGAAGCTTACACTCAAACGACAGCGAAAAC
TTGTACCTTTAAGTAGGAAGGTTGAAAGAAGAGAAAAACGGAGAGAGGAAAAAGCTCTGGTTGCCGCTCAGTTGGACAAT
GCTATCGAGAAAGAGCTGCTGGAGAGGTTGAAACAAGGAGCATATGGCGATATCTACAATTTCCCAATCCATGCCTTTGA
TAAGGCTCTAGAGCGGCAAGATGAGGAGAGCGAAACAGATTCTTCTGAGGGGGAAGAGGAGGTGGAAGACGAGGACTCTG
GACAGAGAGAATTTGTTGAAGATGAAGAGATCGATGAGAGTGACATCAGTGACTTTGAGGACATGGATAAACTGAATGAG
CTCAGCAATGAAGAGCAATCTTCAAGTGCCGAGGAGGAGTCTGGGGACGAGGTAGAAGAGGAGAAAGAAGGCCATGCTGT
ATCAAAGTCTAAGGGCAAAACGCCCTTAAAAGGATCAATTAGGAAGAAACGAGCATATGTAGAAATGGAATATGAACAAG
AGACTGAACCAACAGCAAAGGCAAAAACAACA

Alignment

ORF - retro_lcha_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MQHDDVIWDIIGNKQFCSFKVRTKTQSFCRNEYNITGLCNRSSCPLANSQYATVREEKGQCYLYMKMIER
          MQHDDVIWDIIGNKQFCSFKVRTKTQSFCRNEYNITGLCNRSSCPLANSQYATVREEKGQCYLYMKMIER
Retrocopy MQHDDVIWDIIGNKQFCSFKVRTKTQSFCRNEYNITGLCNRSSCPLANSQYATVREEKGQCYLYMKMIER

Parental  AAFPARLWERVKLSKNYEKALEQIDENLIYWPRFIRHKCKQRFTKITQYLIRIRKLTLKRQRKLVPLSRK
          AAFPARLWERVKLSKNYEKALEQIDENLIYWPRFIRHKCKQRFTKITQYLIRIRKLTLKRQRKLVPLSRK
Retrocopy AAFPARLWERVKLSKNYEKALEQIDENLIYWPRFIRHKCKQRFTKITQYLIRIRKLTLKRQRKLVPLSRK

Parental  VERREKRREEKALVAAQLDNAIEKELLERLKQGAYGDIYNFPIHAFDKALERQDEESETDSSEGEEEVED
          VERREKRREEKALVAAQLDNAIEKELLERLKQGAYGDIYNFPIHAFDKALERQDEESETDSSEGEEEVED
Retrocopy VERREKRREEKALVAAQLDNAIEKELLERLKQGAYGDIYNFPIHAFDKALERQDEESETDSSEGEEEVED

Parental  EDSGQREFVEDEEIDESDISDFEDMDKLNELSNEEQSSSAEEESGDEVEEEKEGHAVSKSKGKTPLKGSI
          EDSGQREFVEDEEIDESDISDFEDMDKLNELSNEEQSSSAEEESGDEVEEEKEGHAVSKSKGKTPLKGSI
Retrocopy EDSGQREFVEDEEIDESDISDFEDMDKLNELSNEEQSSSAEEESGDEVEEEKEGHAVSKSKGKTPLKGSI

Parental  RKKRAYVEMEYEQETEPTAKAKTT
          RKKRAYVEMEYEQETEPTAKAKTT
Retrocopy RKKRAYVEMEYEQETEPTAKAKTT

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	0.04 RPM	4.40 RPM
DRP000627_kidney	0.04 RPM	5.63 RPM
DRP000627_pectoral_fin	0.18 RPM	5.28 RPM
DRP000627_pelvic_fin	0.03 RPM	8.60 RPM
DRP000627_pharynx	0.07 RPM	6.01 RPM
DRP000627_tail_muscle	0.08 RPM	5.46 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_67 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009081	5 retrocopies	retro_chof_2336, retro_chof_2538, retro_chof_531, retro_chof_867, retro_chof_948,
Dasypus novemcinctus	ENSDNOG00000008424	1 retrocopy	retro_dnov_624,
Latimeria chalumnae	ENSLACG00000018758	1 retrocopy	retro_lcha_67 ,
Macropus eugenii	ENSMEUG00000006945	1 retrocopy	retro_meug_1291,
Myotis lucifugus	ENSMLUG00000002758	1 retrocopy	retro_mluc_590,
Oryctolagus cuniculus	ENSOCUG00000008735	3 retrocopies	retro_ocun_1053, retro_ocun_1298, retro_ocun_908,
Sus scrofa	ENSSSCG00000015832	1 retrocopy	retro_sscr_917,