RetrogeneDB ID: retro_gmor_15

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: contig40242:72..462(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGMOG00000020343
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rps24 (1 of 2)
• Ensembl ID: ENSGMOG00000012595
• Aliases: None
• Description: ribosomal protein S24 [Source:ZFIN;Acc:ZDB-GENE-040109-5]

Sequence

>retro_gmor_15
AATGACACAGTGACTGTCAGGACCCGGAAATTCATGACGAACCGGCTGCTCCAGAGGAAGCAAATGGTCGTCGATGTCCT
GCATCCTGGCAAGGCCACAGTCCCAAAGACTGAAATCAGGGAGAAACTAGCAAAAATGTACAAGACCACTCCCGATGTGG
TCTTTGTCTTTGGCTTCAGGACCCAGTTCGGAGGTGGCAAGACTACAGGCTTCGCCATGGTCTACGACTCGTTAGACTAC
GCCAAGAAGAACGAGCCCAAGCACAGACTGGCCAGACATGGTCTGTACGAGAAGAAGAAGTCCTCCAGGAAACAGCGCAA
GGAGCGAAAGAACAGAATGAAGAAAGTACGAGGCACCAAGAAGGCGGCTGTGGGGGCTGCTGGCAAAAAG

Alignment

ORF - retro_gmor_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  NDTVTVRTRKFMTNRLLQRKQMVVDVLHPGKATVPKTEIREKLAKMYKTTPDVVFVFGFRTQFGGGKTTG
          NDTVTVRTRKFMTNRLLQRKQMVVDVLHPGKATVPKTEIREKLAKMYKTTPDVVFVFGFRTQFGGGKTTG
Retrocopy NDTVTVRTRKFMTNRLLQRKQMVVDVLHPGKATVPKTEIREKLAKMYKTTPDVVFVFGFRTQFGGGKTTG

Parental  FAMVYDSLDYAKKNEPKHRLARHGLYEKKKSSRKQRKERKNRMKKVRGTKKAAVGAAGKK
          FAMVYDSLDYAKKNEPKHRLARHGLYEKKKSSRKQRKERKNRMKKVRGTKKAAVGAAGKK
Retrocopy FAMVYDSLDYAKKNEPKHRLARHGLYEKKKSSRKQRKERKNRMKKVRGTKKAAVGAAGKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Gadus morhua was not studied using RNA-Seq expression data.

ChIP-Seq

Gadus morhua was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_gmor_15 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_15 was not experimentally validated.

Homology

Retrocopy orthology:

Gadus morhua 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 27 parental genes, and 166 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017818	17 retrocopies	retro_amel_1043, retro_amel_1258, retro_amel_1303, retro_amel_1397, retro_amel_145, retro_amel_1814, retro_amel_1832, retro_amel_225, retro_amel_24, retro_amel_251, retro_amel_328, retro_amel_331, retro_amel_515, retro_amel_718, retro_amel_768, retro_amel_81, retro_amel_886,
Bos taurus	ENSBTAG00000013264	9 retrocopies	retro_btau_1137, retro_btau_1311, retro_btau_1562, retro_btau_285, retro_btau_467, retro_btau_577, retro_btau_586, retro_btau_788, retro_btau_980,
Cavia porcellus	ENSCPOG00000020096	3 retrocopies	retro_cpor_1333, retro_cpor_14, retro_cpor_923,
Dasypus novemcinctus	ENSDNOG00000010243	18 retrocopies	retro_dnov_1299, retro_dnov_1305, retro_dnov_1394, retro_dnov_1444, retro_dnov_1470, retro_dnov_1471, retro_dnov_168, retro_dnov_1889, retro_dnov_1920, retro_dnov_1985, retro_dnov_2074, retro_dnov_2357, retro_dnov_288, retro_dnov_309, retro_dnov_551, retro_dnov_73, retro_dnov_782, retro_dnov_92,
Dipodomys ordii	ENSDORG00000000189	4 retrocopies	retro_dord_248, retro_dord_498, retro_dord_717, retro_dord_766,
Equus caballus	ENSECAG00000016939	5 retrocopies	retro_ecab_239, retro_ecab_398, retro_ecab_422, retro_ecab_514, retro_ecab_746,
Echinops telfairi	ENSETEG00000007481	32 retrocopies	retro_etel_1119, retro_etel_1242, retro_etel_1274, retro_etel_1339, retro_etel_1395, retro_etel_1663, retro_etel_1688, retro_etel_1783, retro_etel_1800, retro_etel_1806, retro_etel_183, retro_etel_1901, retro_etel_1934, retro_etel_1978, retro_etel_1991, retro_etel_2040, retro_etel_2104, retro_etel_223, retro_etel_287, retro_etel_289, retro_etel_369, retro_etel_422, retro_etel_476, retro_etel_503, retro_etel_523, retro_etel_67, retro_etel_744, retro_etel_752, retro_etel_815, retro_etel_904, retro_etel_91, retro_etel_94,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Homo sapiens	ENSG00000138326	3 retrocopies	retro_hsap_1511, retro_hsap_526, retro_hsap_658,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15 ,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439, retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Microcebus murinus	ENSMICG00000005951	7 retrocopies	retro_mmur_1308, retro_mmur_132, retro_mmur_1338, retro_mmur_1636, retro_mmur_217, retro_mmur_583, retro_mmur_902,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Monodelphis domestica	ENSMODG00000025091	3 retrocopies	retro_mdom_1303, retro_mdom_1706, retro_mdom_1914,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Mus musculus	ENSMUSG00000025290	13 retrocopies	retro_mmus_1101, retro_mmus_1462, retro_mmus_1589, retro_mmus_1592, retro_mmus_1599, retro_mmus_2134, retro_mmus_2332, retro_mmus_2497, retro_mmus_2984, retro_mmus_3162, retro_mmus_321, retro_mmus_3233, retro_mmus_602,
Ornithorhynchus anatinus	ENSOANG00000006329	1 retrocopy	retro_oana_54,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16,
Otolemur garnettii	ENSOGAG00000011005	3 retrocopies	retro_ogar_1000, retro_ogar_2, retro_ogar_2130,
Pongo abelii	ENSPPYG00000002304	1 retrocopy	retro_pabe_184,
Pan troglodytes	ENSPTRG00000002666	10 retrocopies	retro_ptro_1023, retro_ptro_1114, retro_ptro_1257, retro_ptro_1555, retro_ptro_1885, retro_ptro_2376, retro_ptro_362, retro_ptro_393, retro_ptro_478, retro_ptro_983,
Rattus norvegicus	ENSRNOG00000010189	1 retrocopy	retro_rnor_206,
Sarcophilus harrisii	ENSSHAG00000008090	3 retrocopies	retro_shar_276, retro_shar_303, retro_shar_697,
Sus scrofa	ENSSSCG00000010328	8 retrocopies	retro_sscr_1212, retro_sscr_14, retro_sscr_242, retro_sscr_289, retro_sscr_491, retro_sscr_564, retro_sscr_718, retro_sscr_902,
Ictidomys tridecemlineatus	ENSSTOG00000013000	4 retrocopies	retro_itri_167, retro_itri_376, retro_itri_528, retro_itri_728,
Tarsius syrichta	ENSTSYG00000006715	1 retrocopy	retro_tsyr_1919,
Tursiops truncatus	ENSTTRG00000007845	3 retrocopies	retro_ttru_1462, retro_ttru_740, retro_ttru_86,