RetrogeneDB ID: retro_ttru_875

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_436:214199..215310(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000014400
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSTTRG00000004331
• Aliases: None
• Description: 3-oxoacid CoA transferase 1 [Source:HGNC Symbol;Acc:8527]

Sequence

>retro_ttru_875
ATCGTCTGCTCGTACTTGGTGGAGAACTCGCTCTGCGAGCACCGGTACCTGGCGGGCGAGCTGGAGCTGGAGATCACACC
CCAGGGCACCCTGGCCGAGCGCATCCGCGCGGGGGGGAGCCGGCGTGCCCGCCTTCCACATCCCCACGGCCTGCGGGACC
CTGGCCCAGGAGGGAGGCACACCCAGCAAGTCCTTAGAGGACGGCCACATCGCCATCCTGAGTCAGCCCAGGGAGGTGAG
GGAGTTCCACGGACAGCACTACCTTCTGGAGCACGACGTCACGGCCGGTTTTGCTTTGGTGAAAGGGTGGAAGGCCGACC
GGGCAGGAAACGTCATCTTCAGGGCCAGCGCCAGGAACTTCAACGTGCCCATGTGCAAAGCTGCGAGAACCTCAGTGGTG
GAGATTGAAGAAATTGTGGACCTGGGGCCGTTTGCCCCAGAGGACATCCATGTTCCTAACATTTACTTAGATCGAGGAAT
ACAGGGGGGAAAATATGAGAAAAGAAATGAGCGTTTAACGATGCGGAAAGAGGATGATGAAATATGCAAGTCTGCAGATA
GTATAAGGACACGGATCCTCAAGCAGGCAGCTCTTGACTTTGAGGACGGCCTGTGTGCCAGTTTGGGCATAGGAATCCCT
CTTCTGGCCACCAGCTACATCAGCCCCACTATAACCGTTCATCTTCACAGTGAAAATGGAATCTTGGGCTTGGGTCCGTT
CCCACTGAAAGAGGAGGTGGACGCAGATCTCAACAACGCGGGCAAGCACACAGTGATCCTTCTTCCTGGGGGCTGTTTTT
TCTCCAGCGATGAATCATTTGCCATGATTCGAGGGGGACACATCGACCTAACCTTGCTGGGAGCCATGCAGGTTTCCAAA
TACGGTGACCTGGCTAACTGGATGATACCCGGCAAGAAGGTGAAAGGAATGGGGGGTGCGATGGATCTGGTGTCCAGTAC
CGAGACCAGAGTGATGGTCACCATGGAGCACTCCACCAAGGCCAGTGAACCCAGAATTTTGGAGAAATGTACCATGCCGC
TGAATGGAAAGCGGTGTGTGGACTGAATCATCACCGAGAAGGCCGTGTTTGACATGCACAGGAAGGGAGGA

Alignment

ORF - retro_ttru_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.05 %
• Parental protein coverage: 71.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVSSYVGENAEFERQYLSGELEVELTPQGTLAERIRAGG-AGVPAFYTSTGYGTLVQEGGSPIKYNKDGS
          .V.SY..EN...E..YL.GELE.E.TPQGTLAERIRAGG.AGVPAF...T..GTL.QEGG.P.K...DG.
Retrocopy IVCSYLVENSLCEHRYLAGELELEITPQGTLAERIRAGG>AGVPAFHIPTACGTLAQEGGTPSKSLEDGH

Parental  IAIASKPREVREFNGQHFILEEAITGDFALVKAWKADRAGNVIFRKSARNFNLPMCKAAETTVVEVEEIV
          IAI.S.PREVREF.GQH..LE...T..FALVK.WKADRAGNVIFR.SARNFN.PMCKAA.T.VVE.EEIV
Retrocopy IAILSQPREVREFHGQHYLLEHDVTAGFALVKGWKADRAGNVIFRASARNFNVPMCKAARTSVVEIEEIV

Parental  DIGSFAPEDIHIPKIYVHRLIKGEKYEKRIERLSIRKEEDVKTTSGKPGDNVRERIIKRAALEFEDGMYA
          D.G.FAPEDIH.P.IY..R.I.G.KYEKR.ERL..R..ED......K..D..R.RI.K.AAL.FEDG..A
Retrocopy DLGPFAPEDIHVPNIYLDRGIQGGKYEKRNERLTMR-KEDDEIC--KSADSIRTRILKQAALDFEDGLCA

Parental  NLGIGIPLLASNFISPSMTVHLQSENGVLGLGPYPLKNEVDADLINAGKETVTVLPGASYFSSDESFAMI
          .LGIGIPLLA...ISP..TVHL.SENG.LGLGP.PLK.EVDADL.NAGK.TV..LPG...FSSDESFAMI
Retrocopy SLGIGIPLLATSYISPTITVHLHSENGILGLGPFPLKEEVDADLNNAGKHTVILLPGGCFFSSDESFAMI

Parental  RGGHVNLTMLGAMQVSKYGDLANWMIPGKMVKGMGGAMDLVSSAKTKVVVTMEHSAKGNAHKIMEKCTLP
          RGGH..LT.LGAMQVSKYGDLANWMIPGK.VKGMGGAMDLVSS..T.V.VTMEHS.K.....I.EKCT.P
Retrocopy RGGHIDLTLLGAMQVSKYGDLANWMIPGKKVKGMGGAMDLVSSTETRVMVTMEHSTKASEPRILEKCTMP

Parental  LTGKQCVNRIITEKAVFDVDNKKG
          L.GK.CV..IITEKAVFD...K.G
Retrocopy LNGKRCVD*IITEKAVFDMHRKGG

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_875 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_875 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033186	2 retrocopies	retro_btau_1243, retro_btau_1302,
Dipodomys ordii	ENSDORG00000016318	1 retrocopy	retro_dord_282,
Equus caballus	ENSECAG00000018312	1 retrocopy	retro_ecab_511,
Homo sapiens	ENSG00000083720	1 retrocopy	retro_hsap_14,
Gorilla gorilla	ENSGGOG00000025087	1 retrocopy	retro_ggor_378,
Myotis lucifugus	ENSMLUG00000009431	1 retrocopy	retro_mluc_194,
Nomascus leucogenys	ENSNLEG00000016656	1 retrocopy	retro_nleu_2438,
Oryctolagus cuniculus	ENSOCUG00000009231	1 retrocopy	retro_ocun_672,
Otolemur garnettii	ENSOGAG00000009909	2 retrocopies	retro_ogar_2773, retro_ogar_2781,
Pongo abelii	ENSPPYG00000015428	2 retrocopies	retro_pabe_336, retro_pabe_478,
Pan troglodytes	ENSPTRG00000016829	1 retrocopy	retro_ptro_140,
Rattus norvegicus	ENSRNOG00000043094	2 retrocopies	retro_rnor_2177, retro_rnor_2256,
Ictidomys tridecemlineatus	ENSSTOG00000008271	1 retrocopy	retro_itri_747,
Tarsius syrichta	ENSTSYG00000013641	1 retrocopy	retro_tsyr_1455,
Tursiops truncatus	ENSTTRG00000004331	1 retrocopy	retro_ttru_875 ,
Vicugna pacos	ENSVPAG00000002550	1 retrocopy	retro_vpac_556,