RetrogeneDB ID: retro_ttru_1109

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_103371:232986..233714(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSTTRG00000000871
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_ttru_1109
GAAAAGACGGAGCTGATCCAGAAGGGCAAGCTGGCCGAGCAGGCCAAGCGCTATGACGACATGGCCACCTGCATGAAAGC
CGTGATGGAGCAGGGCGCGGAGCTGTCCAACGAGGATGCAACCTGCTCTCGGTGGCCTACAAGAACGTCGGGGGCCACAC
GTCCGCCTGGAGGGTCATCTCGAGCATCGAGCAGAAGACCAACACCTCCGACAAGAAGTTGCAGCCGATTAAGGACTATC
GGGAGAAAGTGGAGTCCGAACTGAAGTCCATCTGCACCACGGTCCTGGAATTGTTGGATAAGTCCTTAATAGCCAATGCA
ACTAATCCAGAGAGTAAGGTCTTCTATCTGAAGATGAAGGGAGATTACTTCCAGTACCTTGCTGAAGTTGCTTGTGGTGA
TGATCAGAAACAAACAATAGATAATTCCCAAGGAGCTTACCAAGAGGCTATTAATATAAGCAAGAAAGAGATGCAACCCA
CACACCCAATACGCCTGGGGCTGGCTCTTAACTTTTCTGTATTTTACTATGAGATCCTTAATAACCCAGAACTTGCCTGC
ACACTGGCTAAAACGGCTTTTGATGAAGCCATTGCAGAATTTGATACACTGAATGAAGACTCATACAAAGACAGCACCCT
CATCATGCAGTTGCTTAGAGACAACCTAACATAATGGACATCAGACAGTGCAGGAGAAGAATGTGATGTGGCAGAAGGGG
CAGAGAAC

Alignment

ORF - retro_ttru_1109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKTELIQK-KLAEQAERYDDMA-CMKAVTEQGAELSNEER-NLLSVAYKNVVGGRRSAWRVISSIEQKTD
          EKTELIQK.KLAEQA.RYDDMA.CMKAV.EQGAELSNE...NLLSVAYKNV.GG..SAWRVISSIEQKT.
Retrocopy EKTELIQKGKLAEQAKRYDDMATCMKAVMEQGAELSNEDA<NLLSVAYKNV-GGHTSAWRVISSIEQKTN

Parental  TSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQ
          TSDKKLQ.IKDYREKVESEL.SICTTVLELLDK.LIANATNPESKVFYLKMKGDYF.YLAEVACGDD.KQ
Retrocopy TSDKKLQPIKDYREKVESELKSICTTVLELLDKSLIANATNPESKVFYLKMKGDYFQYLAEVACGDDQKQ

Parental  TIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDS
          TIDNSQGAYQEA..ISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAE.DTLNEDS
Retrocopy TIDNSQGAYQEAINISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAEFDTLNEDS

Parental  YKDSTLIMQLLRDNLTLWTSDSAGEECDAAEGAEN
          YKDSTLIMQLLRDNLT.WTSDSAGEECD.AEGAEN
Retrocopy YKDSTLIMQLLRDNLT*WTSDSAGEECDVAEGAEN

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_1109 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1109 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 14 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000004925	1 retrocopy	retro_ecab_134,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Felis catus	ENSFCAG00000007854	2 retrocopies	retro_fcat_1702, retro_fcat_771,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mus musculus	ENSMUSG00000076432	10 retrocopies	retro_mmus_1076, retro_mmus_1378, retro_mmus_1926, retro_mmus_2250, retro_mmus_2299, retro_mmus_2471, retro_mmus_2689, retro_mmus_3250, retro_mmus_3308, retro_mmus_406,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Otolemur garnettii	ENSOGAG00000000547	3 retrocopies	retro_ogar_1047, retro_ogar_1732, retro_ogar_39,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,
Tursiops truncatus	ENSTTRG00000000871	4 retrocopies	retro_ttru_1006, retro_ttru_1109 , retro_ttru_1530, retro_ttru_1536,
Tursiops truncatus	ENSTTRG00000007615	1 retrocopy	retro_ttru_762,
Tursiops truncatus	ENSTTRG00000015906	4 retrocopies	retro_ttru_15, retro_ttru_1540, retro_ttru_207, retro_ttru_455,