RetrogeneDB ID: retro_lcha_18

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127089.1:564428..565043(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000011072
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: vbp1 (1 of 2)
• Ensembl ID: ENSLACG00000016144
• Aliases: None
• Description: von Hippel-Lindau binding protein 1 [Source:ZFIN;Acc:ZDB-GENE-050522-494]

Sequence

>retro_lcha_18
ATGATGGTTTTTGGCAAGGGGTGTGAGCTTTCCAAGATGGCGGCGACCAGTGAGAACAGCAATGCTGCAGGAGCCAAGAA
GAGCCATTTAGGCATTCCAGAGGCTGTGTTTGTGGAGGATGTAGACACATTTATGAAGCAGCCAGGGAATGAGACTGCTG
ACATTGTGCTCAAAAAGTTGGATGAACAGTATCAGAAGTATAAATTCATGGAACTTAATCTTGTTCAAAAGAAAAAAAGG
CTAAAAAGTCAGATCCCAGAAATAAAACAGACGCTAGAGATTTTAAAACAGATGCAGAAAAAAAAGGGAACTACAGACCC
AATGGAGACCAGGTTTTTATTGGCAGATAATCTGTATTGTAAAGCCTCAGTTCTTCCTACAGATAAAGTCTGCTTGTGGT
TGGGGGCTAATGTCATGCTGGAGTATGATATTGATGAGGCCCAGGCTTTACTCGAGAAAAACCTGTCAACAGCTACAAGG
AATCTAGAATCACTAGAAGAGAACCTAGATTTCCTCAGAGACCAGTTCACTACCACAGAAGTCAATATGGCCAGAGTTTA
TAACTGGGATGTAAAAAGAAGAAATAAGGATGATCCCACTAAAGCCAGCGCATAG

Alignment

ORF - retro_lcha_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSKMAATSENSNAAGAKKSHLGIPEAVFVEDVDTFMKQPGNETADIVLKKLDEQYQKYKFMELNLVQKKK
          LSKMAATSENSNAAGAKKSHLGIPEAVFVEDVDTFMKQPGNETADIVLKKLDEQYQKYKFMELNLVQKKK
Retrocopy LSKMAATSENSNAAGAKKSHLGIPEAVFVEDVDTFMKQPGNETADIVLKKLDEQYQKYKFMELNLVQKKK

Parental  RLKSQIPEIKQTLEILKHMQKKKGTTDPMETRFLLADNLYCKASVLPTDKVCLWLGVSPTMRTFEFESSL
          RLKSQIPEIKQTLEILK.MQKKKGTTDPMETRFLLADNLYCKASVLPTDKVCLWLG....M.........
Retrocopy RLKSQIPEIKQTLEILKQMQKKKGTTDPMETRFLLADNLYCKASVLPTDKVCLWLGAN-VMLEYDIDEAQ

Parental  KKYHDNISAVPLNKEGKKRSLGFLVEGFPRKQAYMARVYNWDVKRRNKDDPTKAS
          .....N.S....N.E.....L.FL...F......MARVYNWDVKRRNKDDPTKAS
Retrocopy ALLEKNLSTATRNLESLEENLDFLRDQFTTTEVNMARVYNWDVKRRNKDDPTKAS

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	1.92 RPM	0.99 RPM
DRP000627_kidney	1.34 RPM	0.72 RPM
DRP000627_pectoral_fin	3.54 RPM	1.07 RPM
DRP000627_pelvic_fin	3.66 RPM	2.21 RPM
DRP000627_pharynx	2.62 RPM	1.25 RPM
DRP000627_tail_muscle	2.86 RPM	1.56 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_18 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 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009058	2 retrocopies	retro_amel_1232, retro_amel_1346,
Canis familiaris	ENSCAFG00000019639	2 retrocopies	retro_cfam_1030, retro_cfam_573,
Cavia porcellus	ENSCPOG00000013652	1 retrocopy	retro_cpor_466,
Dasypus novemcinctus	ENSDNOG00000019432	1 retrocopy	retro_dnov_694,
Dipodomys ordii	ENSDORG00000004628	2 retrocopies	retro_dord_213, retro_dord_587,
Echinops telfairi	ENSETEG00000017655	2 retrocopies	retro_etel_2085, retro_etel_552,
Latimeria chalumnae	ENSLACG00000016144	1 retrocopy	retro_lcha_18 ,
Loxodonta africana	ENSLAFG00000016507	2 retrocopies	retro_lafr_1200, retro_lafr_163,
Myotis lucifugus	ENSMLUG00000015396	3 retrocopies	retro_mluc_1600, retro_mluc_2019, retro_mluc_986,
Macaca mulatta	ENSMMUG00000015095	1 retrocopy	retro_mmul_124,
Mus musculus	ENSMUSG00000031197	1 retrocopy	retro_mmus_2220,
Nomascus leucogenys	ENSNLEG00000014475	1 retrocopy	retro_nleu_537,
Oryctolagus cuniculus	ENSOCUG00000017448	2 retrocopies	retro_ocun_233, retro_ocun_747,
Otolemur garnettii	ENSOGAG00000016566	1 retrocopy	retro_ogar_3121,
Sarcophilus harrisii	ENSSHAG00000002823	1 retrocopy	retro_shar_7,
Sus scrofa	ENSSSCG00000012811	1 retrocopy	retro_sscr_131,
Ictidomys tridecemlineatus	ENSSTOG00000006684	1 retrocopy	retro_itri_1492,
Tupaia belangeri	ENSTBEG00000007833	5 retrocopies	retro_tbel_3084, retro_tbel_3369, retro_tbel_3652, retro_tbel_553, retro_tbel_632,
Tarsius syrichta	ENSTSYG00000002205	1 retrocopy	retro_tsyr_2032,
Tursiops truncatus	ENSTTRG00000016258	1 retrocopy	retro_ttru_988,