RetrogeneDB ID: retro_lcha_3

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH129897.1:111450..112233(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000004162
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: psmb5 (1 of 2)
• Ensembl ID: ENSLACG00000015194
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 5 [Source:ZFIN;Acc:ZDB-GENE-990415-215]

Sequence

>retro_lcha_3
ATGGCATTGGCAGATGTACTGCGTGTTGAATCAGCGGCTTTTCAGTTTGGTTTGCCCGGCAGTTTGGTTCTGGGACCCGG
GCCGGTGGGCCTGAGCCTGGTGGCACTGAAGCTGATCGGGCTGGGAGAAGAGGAAGAGAACCAAGTCCCGAAAATCAAGT
TTCTACACAGAACCACCACGCTGGCTTTCAAGTTCTTCCATGGTGTGTTGGTGGCGGTGGACTCCCACACCATGGTGGGC
TCTTACATTGATTCACAGACAGTGAAGAAGGTTATCGAGATTAACCCATACCTGCTGGGGACCATGGTGGGTGGCGCAGC
TGACTGCAGCTTCTGGGAGCGCCTCCTGGCCCGACAGTGCTGCATCTATGAGCTAAGGAACAATGAGAGGATCTCTGTGG
CTGCCGCTTCCAAACTGCTGGCCCATATGGTCTACCAGTACAAGGGAATGGGGCTGTCCAAGGGGACGATGATCTGCGGC
TGGGACAAGCAGGGCCCAGGCCTATATTTTGTTGATAGTGAAGGAAACTGGATTACTGGGGACAACTTCTCTGTGGGCTC
CGGGTCAGTCTATGCATACGGTGTCCTGGACCGTGGCTACCACTTTGACCTGAGTGTGGAAGAAGCCAATGACCTGGCCC
GGTGTGCCATCTACCACACCACCTACCGCGATGCATACTCGGGCAGGGTGGTCAACATCTACCATGTGCGGGAGGATGGC
TGGTTCTGCGTCTTTCAGGACAACATCCTCCAGCTGCGTGAGGAGTTCCAAGAAGCTGCCTGA

Alignment

ORF - retro_lcha_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.69 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALADVLRDESVAFRFGLPGGSVLGPGPAGLSLAAPKLIGLGEEEENQAPKIEFLHGTTTLAFKFFHGVL
          MALADVLR.ES.AF.FGLPG..VLGPGP.GLSL.A.KLIGLGEEEENQ.PKI.FLH.TTTLAFKFFHGVL
Retrocopy MALADVLRVESAAFQFGLPGSLVLGPGPVGLSLVALKLIGLGEEEENQVPKIKFLHRTTTLAFKFFHGVL

Parental  VAVDSRATAGSYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLL
          VAVDS....GSYI.SQTVKKVIEINPYLLGTM.GGAADCSFWERLLARQC.IYELRN.ERISVAAASKLL
Retrocopy VAVDSHTMVGSYIDSQTVKKVIEINPYLLGTMVGGAADCSFWERLLARQCCIYELRNNERISVAAASKLL

Parental  ANMVYQYKGMGLSMGTMICGWDKRGPGLYFVDSEGNRITGDNFSVGSGSVYAYGVLDRGYHFDLSVEEAY
          A.MVYQYKGMGLS.GTMICGWDK.GPGLYFVDSEGN.ITGDNFSVGSGSVYAYGVLDRGYHFDLSVEEA.
Retrocopy AHMVYQYKGMGLSKGTMICGWDKQGPGLYFVDSEGNWITGDNFSVGSGSVYAYGVLDRGYHFDLSVEEAN

Parental  DLARRAIYHATYRDAYSGGVVNIYHVREDGWFRVFQDDVLELHEEFQEAA
          DLAR.AIYH.TYRDAYSG.VVNIYHVREDGWF.VFQD..L.L.EEFQEAA
Retrocopy DLARCAIYHTTYRDAYSGRVVNIYHVREDGWFCVFQDNILQLREEFQEAA

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	39.54 RPM
DRP000627_kidney	0.00 RPM	35.07 RPM
DRP000627_pectoral_fin	0.00 RPM	37.13 RPM
DRP000627_pelvic_fin	0.00 RPM	62.45 RPM
DRP000627_pharynx	0.00 RPM	49.94 RPM
DRP000627_tail_muscle	0.00 RPM	44.54 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_3 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008299	4 retrocopies	retro_cjac_1983, retro_cjac_35, retro_cjac_3888, retro_cjac_4076,
Homo sapiens	ENSG00000100804	2 retrocopies	retro_hsap_1634, retro_hsap_95,
Gorilla gorilla	ENSGGOG00000026856	2 retrocopies	retro_ggor_1232, retro_ggor_156,
Latimeria chalumnae	ENSLACG00000015194	1 retrocopy	retro_lcha_3 ,
Macropus eugenii	ENSMEUG00000003572	1 retrocopy	retro_meug_28,
Myotis lucifugus	ENSMLUG00000014281	1 retrocopy	retro_mluc_1428,
Macaca mulatta	ENSMMUG00000006007	1 retrocopy	retro_mmul_1558,
Mus musculus	ENSMUSG00000022193	1 retrocopy	retro_mmus_2887,
Nomascus leucogenys	ENSNLEG00000014891	2 retrocopies	retro_nleu_1063, retro_nleu_2936,
Oryctolagus cuniculus	ENSOCUG00000013109	1 retrocopy	retro_ocun_176,
Pongo abelii	ENSPPYG00000005654	1 retrocopy	retro_pabe_171,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616,