RetrogeneDB ID: retro_lcha_51

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126962.1:964957..965419(-)
• Located in intron of: ENSLACG00000014056

Retrocopy information

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

Parental gene information

• Parental gene symbol: SOD1
• Ensembl ID: ENSLACG00000013736
• Aliases: None
• Description: Superoxide dismutase [Cu-Zn] [Source:UniProtKB/TrEMBL;Acc:H3B131]

Sequence

>retro_lcha_51
ATGTCGGGGCTGAAGGCTGTCTGTGTGCTGAAGGGTACTGAGCCTGTTTCCAGCACTGTTTGCTTCGAGGAGAAGGATGG
TGCAGTAACTATAAAGGGGAACATTAAAGGATTGGCTCCTGGGAAACATGGCTTCCATGTCCATGCGTTTGGGGACAATA
CAAATGGCTGTGTGAGTGCGGGACCCCATTTTAACCCCCATAACAAACAGCATGGTGCACCAAATGATGAAAACAGGCAT
GCGGGAGACCTCGGCAATGTGCTGGCCAATGATCAAGGCATAGCAGAATTTACTATAGTGGACCGACAGATCTCACTGAC
AGGGCCTTCGTCCATCATTGGACGCACCATGGTGATCCATGAGAAGGAAGATGACTTGGGGAAAGGAGGAAGTGATGAGA
GCAAGACAACTGGGAATGCTGGTAGCCGATTAGCTTGTGGTGTTGTTGGAATAGCTCAGACC

Alignment

ORF - retro_lcha_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGLKAVCVLKGTEPVSGTVCFEEKDGAVTIKGNIKGLAPGKHGFHVHAFGDNTNGCVSAGPHFNPHNKQ
          MSGLKAVCVLKGTEPVS.TVCFEEKDGAVTIKGNIKGLAPGKHGFHVHAFGDNTNGCVSAGPHFNPHNKQ
Retrocopy MSGLKAVCVLKGTEPVSSTVCFEEKDGAVTIKGNIKGLAPGKHGFHVHAFGDNTNGCVSAGPHFNPHNKQ

Parental  HGAPDDENRHAGDLGNVLANDQGIAEFTIVDQQISLTGPSSIIGRTMVIHEKEDDLGKGGNDESKTTGNA
          HGAP.DENRHAGDLGNVLANDQGIAEFTIVD.QISLTGPSSIIGRTMVIHEKEDDLGKGG.DESKTTGNA
Retrocopy HGAPNDENRHAGDLGNVLANDQGIAEFTIVDRQISLTGPSSIIGRTMVIHEKEDDLGKGGSDESKTTGNA

Parental  GSRLACGVVGIAQT
          GSRLACGVVGIAQT
Retrocopy GSRLACGVVGIAQT

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	0.33 RPM	22.42 RPM
DRP000627_kidney	0.42 RPM	22.07 RPM
DRP000627_pectoral_fin	0.08 RPM	40.92 RPM
DRP000627_pelvic_fin	0.65 RPM	76.22 RPM
DRP000627_pharynx	0.21 RPM	18.93 RPM
DRP000627_tail_muscle	0.17 RPM	13.54 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_51 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 26 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018854	1 retrocopy	retro_btau_40,
Canis familiaris	ENSCAFG00000008859	1 retrocopy	retro_cfam_1515,
Callithrix jacchus	ENSCJAG00000008983	3 retrocopies	retro_cjac_1477, retro_cjac_1986, retro_cjac_652,
Dasypus novemcinctus	ENSDNOG00000006512	1 retrocopy	retro_dnov_816,
Dipodomys ordii	ENSDORG00000013850	3 retrocopies	retro_dord_217, retro_dord_41, retro_dord_603,
Erinaceus europaeus	ENSEEUG00000015905	1 retrocopy	retro_eeur_305,
Felis catus	ENSFCAG00000002225	2 retrocopies	retro_fcat_1260, retro_fcat_422,
Homo sapiens	ENSG00000142168	3 retrocopies	retro_hsap_1637, retro_hsap_3591, retro_hsap_4117,
Gorilla gorilla	ENSGGOG00000015554	4 retrocopies	retro_ggor_1238, retro_ggor_2421, retro_ggor_2690, retro_ggor_2763,
Latimeria chalumnae	ENSLACG00000013736	1 retrocopy	retro_lcha_51 ,
Loxodonta africana	ENSLAFG00000010708	1 retrocopy	retro_lafr_127,
Microcebus murinus	ENSMICG00000005253	2 retrocopies	retro_mmur_378, retro_mmur_573,
Macaca mulatta	ENSMMUG00000001711	2 retrocopies	retro_mmul_1563, retro_mmul_2372,
Monodelphis domestica	ENSMODG00000021041	1 retrocopy	retro_mdom_1376,
Mus musculus	ENSMUSG00000022982	1 retrocopy	retro_mmus_2742,
Nomascus leucogenys	ENSNLEG00000003545	3 retrocopies	retro_nleu_1324, retro_nleu_302, retro_nleu_584,
Otolemur garnettii	ENSOGAG00000014646	3 retrocopies	retro_ogar_27, retro_ogar_3364, retro_ogar_702,
Ochotona princeps	ENSOPRG00000007008	1 retrocopy	retro_opri_1190,
Pongo abelii	ENSPPYG00000011354	2 retrocopies	retro_pabe_1353, retro_pabe_3370,
Pan troglodytes	ENSPTRG00000013847	3 retrocopies	retro_ptro_1107, retro_ptro_2431, retro_ptro_2796,
Pteropus vampyrus	ENSPVAG00000005216	2 retrocopies	retro_pvam_281, retro_pvam_563,
Sarcophilus harrisii	ENSSHAG00000004195	1 retrocopy	retro_shar_278,
Ictidomys tridecemlineatus	ENSSTOG00000004434	1 retrocopy	retro_itri_1342,
Tupaia belangeri	ENSTBEG00000007333	4 retrocopies	retro_tbel_2131, retro_tbel_3531, retro_tbel_3611, retro_tbel_429,
Tarsius syrichta	ENSTSYG00000011342	17 retrocopies	retro_tsyr_1055, retro_tsyr_1064, retro_tsyr_1082, retro_tsyr_1112, retro_tsyr_1143, retro_tsyr_1176, retro_tsyr_1262, retro_tsyr_1275, retro_tsyr_1295, retro_tsyr_1369, retro_tsyr_1378, retro_tsyr_1590, retro_tsyr_2107, retro_tsyr_365, retro_tsyr_402, retro_tsyr_823, retro_tsyr_831,
Vicugna pacos	ENSVPAG00000012396	1 retrocopy	retro_vpac_168,