RetrogeneDB ID: retro_ttru_1518

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_115214:35776..36976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3
• Ensembl ID: ENSTTRG00000010880
• Aliases: None
• Description: ribosomal protein L3 [Source:HGNC Symbol;Acc:10332]

Sequence

>retro_ttru_1518
ATGTCTCACAGGAAGTTCTCCACTCCCAGGCATGGGTCCCTGGGCTTTCTGCCTCAGAAGCGCAGCAGCCGGCACCATGG
GAAGGTGAAGAGCTTCCCCGAGGATGACTCTTCCAAGCCCGTGCACCTCACAGCCTTCCTCGGCTACAAGGCTGGCATGA
CCCACATTGTGAGGGAGGTTGATAGGCCAGGGTCCAAGGTGAACAAGAAGGAAGTTGTGGAGGCTGTGACCATCGTGGAG
ACGCCACCCATGGTCATTGTGGGCTACATGGAAACACCTCGAGGCCTCCGGACCTTTAAGACCATCTTTGCTGAGCACAT
CAGTGATGAATGCAAAAGACGCTTCTATAACAACTGGCATAAATCTAAGAAGAAGGCCTTCACCAAATACTGCAAGAAGT
GGCAGGATGTAGATGGCAAGAAGCAGCTGGAGAGGGACTTCAGCAGCTTGAAGAAGTACTACCAGGTCATTCATGTCATT
GCCCACACCCAGATGCGCCTGCTTCCTCTACGCCAGAAGAAGGCCCACCTCATGGAGATCCGGCTGAATGGAGGCACTGA
GGCCGAAAAACTGGACTGGGCCCGAGAGAGGCTAGAGCAGCAGGTCCCTGTGAACCAAGTGTTTGGGCAGGATGAGATGA
TTGATGTCATTGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGCCGTTGGCACACCAAGAAGCTGCCCCGTAAG
ACCCACCGAGGGCTGCGCAAGGTTACCTGTATTGGGGCGTGGCGTCCTGCACGGGTGGCCTTCTCTGTGGCTCAGGCCGG
GCAGAAAGGCTACCATCACCACACCGAGATCAACAAGAAGATCTACAAGATTGGCCAGGGCTACCTCATCAAGGATGGCA
AACTGATCAAGAACAATGCCTTTACTGATTATGATCTGTCTGACAAGAGCATCAACCCTCCGGGTGGCTTTGTCCACTAC
GGTGAAGTGACCAATGACTTTGTCATGATCAAAGGCTGCGTGGTAGGAACCAAGAAGCAAGTGCTCACCCTTGGCAAGTC
CTTGCTGGTGCAGACCAAACAGCGGGCCCTGGAGAAGATTGACCTTAAGTTTATTGACACCACCTCCAAATTTGGCCATG
GCTGTTTCCAGACTGTGGAGGAGAAGAAAGCGTTCATGGGACCATTTAAGAAGGACCGAATTGCAAAGGAAGAAGGGGCC

Alignment

ORF - retro_ttru_1518 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDSCKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
          MSHRKFS.PRHGSLGFLP.KRSSRH.GKVKSFP.DDS.KPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
Retrocopy MSHRKFSTPRHGSLGFLPQKRSSRHHGKVKSFPEDDSSKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK

Parental  EVVEAVTIVETPPMVIVGIVGYVETPRGLRTFKTIFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDV
          EVVEAVTIVETPPMV...IVGY.ETPRGLRTFKTIFAEHISDECKRRFY.NWHKSKKKAFTKYCKKWQDV
Retrocopy EVVEAVTIVETPPMV---IVGYMETPRGLRTFKTIFAEHISDECKRRFYNNWHKSKKKAFTKYCKKWQDV

Parental  DGKKQLERDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVN-V
          DGKKQLERDFSS.KKY.QVI.VIAHTQMRLLPLRQKKAHLMEI..NGGT.AEKLDWARERLEQQVPVN.V
Retrocopy DGKKQLERDFSSLKKYYQVIHVIAHTQMRLLPLRQKKAHLMEIRLNGGTEAEKLDWARERLEQQVPVNQV

Parental  FGQDEMIDVIGVT-GKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEI
          FGQDEMIDVIGVT.GKGYKGVTSRWHTKKLPRKTHRGLRKV.CIGAW.PARVAFSVA.AGQKGYHH.TEI
Retrocopy FGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVTCIGAWRPARVAFSVAQAGQKGYHHHTEI

Parental  NKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKS
          NKKIYKIGQGYLIKDGKLIKNNA.TDYDLSDKSINP.GGFVHYGEVTNDFVM.KGCVVGTKK.VLTL.KS
Retrocopy NKKIYKIGQGYLIKDGKLIKNNAFTDYDLSDKSINPPGGFVHYGEVTNDFVMIKGCVVGTKKQVLTLGKS

Parental  LLVQTKRRALEKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA
          LLVQTK.RALEKIDLKFIDTTSKFGHG.FQTVEEKKAFMGP.KKDRIAKEEGA
Retrocopy LLVQTKQRALEKIDLKFIDTTSKFGHGCFQTVEEKKAFMGPFKKDRIAKEEGA

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1518 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1518 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 15 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003228	3 retrocopies	retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris	ENSCAFG00000001346	1 retrocopy	retro_cfam_97,
Callithrix jacchus	ENSCJAG00000016276	6 retrocopies	retro_cjac_1198, retro_cjac_1972, retro_cjac_2157, retro_cjac_2264, retro_cjac_3079, retro_cjac_823,
Equus caballus	ENSECAG00000020665	1 retrocopy	retro_ecab_897,
Gorilla gorilla	ENSGGOG00000002326	10 retrocopies	retro_ggor_1043, retro_ggor_1295, retro_ggor_1582, retro_ggor_1822, retro_ggor_2329, retro_ggor_2616, retro_ggor_2713, retro_ggor_2736, retro_ggor_2955, retro_ggor_36,
Macropus eugenii	ENSMEUG00000009789	26 retrocopies	retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Macaca mulatta	ENSMMUG00000010029	4 retrocopies	retro_mmul_1170, retro_mmul_149, retro_mmul_2334, retro_mmul_973,
Monodelphis domestica	ENSMODG00000009539	2 retrocopies	retro_mdom_380, retro_mdom_408,
Nomascus leucogenys	ENSNLEG00000015234	2 retrocopies	retro_nleu_1038, retro_nleu_1449,
Oryctolagus cuniculus	ENSOCUG00000027712	4 retrocopies	retro_ocun_105, retro_ocun_179, retro_ocun_1893, retro_ocun_558,
Otolemur garnettii	ENSOGAG00000000032	7 retrocopies	retro_ogar_1264, retro_ogar_1679, retro_ogar_2096, retro_ogar_2122, retro_ogar_2448, retro_ogar_3431, retro_ogar_960,
Pongo abelii	ENSPPYG00000011837	10 retrocopies	retro_pabe_1113, retro_pabe_1861, retro_pabe_2167, retro_pabe_2743, retro_pabe_2985, retro_pabe_3170, retro_pabe_3318, retro_pabe_3349, retro_pabe_3696, retro_pabe_3761,
Rattus norvegicus	ENSRNOG00000016896	2 retrocopies	retro_rnor_1333, retro_rnor_731,
Sarcophilus harrisii	ENSSHAG00000003212	2 retrocopies	retro_shar_154, retro_shar_662,
Tursiops truncatus	ENSTTRG00000010880	2 retrocopies	retro_ttru_1266, retro_ttru_1518 ,