RetrogeneDB ID: retro_ttru_410

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2172:39595..40806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX5
• Ensembl ID: ENSTTRG00000016432
• Aliases: None
• Description: sorting nexin 5 [Source:HGNC Symbol;Acc:14969]

Sequence

>retro_ttru_410
ATGGCCACAGTTCCCAAGTTGCTGCAGCAGCAGGAGGAGGAACACAGCAAGCTGAGATCTGTATCAGTGGACCTGAATGT
TGATCCCTTGCTTCAGACTGACATATCTTATGCACTCAGTGAGAGAGATAAAGTCAAATTTACAGTACACACCAAGACCA
CGCTGCCCACGTTTCAGAGCCCAGAGTTTTCTGTTACAAGGCAACATGAAGATTTTGTGTGGCTACATGACACTCTTATT
GAAACTACAGACTACGCTGGGCTTATTATTCCGCCCGCACCTGCAAAGCCTGACTTCAATGGCCCTTGAGAGAAGATGCA
GAAACTGGGAGAGGGTGAAGGGTTTATGACCAAAGAAGAATTTGCCAAGATGAAGCAAGAGCTGGAAGCTGAGTATCTCA
TGGTCTTCAAGAAGACTGTGTCCTCCCGTGAAGTCTCTCTTCAGCGGCTCTCCTCTCACCCTGTTCTCAGTAATGATTGC
AACTTTCACATTTTCCTGGAATATGATCAAGATCTAAGTGTTAGGCAGAAAAATACCAAAGAGATGTTTGGTGGCTTTTT
CAAAAGTGTGTTGAAAGCACTGATGAAGTCCTTTTTTCAGGAGTTGTGGAGGTAGATGACTTCTTTGAACAAGAGAGGTA
TTTCCTCAGTAACTATTATGATAGGATCAAGGGTTCCTTTGCAAAGGCCGACAGAATGACCAGCGCTAATAAAAATGTAG
CAGACGGTTACATCCTCACCGCAGCCTGCTTGCATAGCCTGGCTTTAGAAGAGCCCACGGTCATCAGAAAGTACCTACTG
AAGGTGGCTGAGCTATCTGAAAAACTTAGGAAGGTAGAGAGTCGAGTCTCCTCAGATGAAGACTTAAAGCTGACAGAGCT
CCTCCGATACTACATGCTCAACATAGAGGCTGCTAAGGATCTCTTATATAGACGCACCGAAGCCCTCATTGACTATGAGA
ATTCAAACAAGGTGCTGGATAAGGCCTGGTTAAAAAGCAAAGACGTCAAGCTGGCTGAGGCATACCAGCAGGAATACTGC
CAGAAATTTGAACAGCTTTCTGAATCTGCGAAAGAAGAGCTAATCAATTTCAAACAAAAGAGAGTGGCAGCATTTAGGAA
GAATCTGATTGAAATGTCTGAACTGGAAATAAAGCATGCCAGGAACAACATCTCCTTCCTGCAGAGCTGCATTGACTTGT
TCAAGAACAAC

Alignment

ORF - retro_ttru_410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVPELLQQQEEDRSKLRSVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHE
          MA.VP.LLQQQEE..SKLRSVSVDLNVDP.LQ.DI..ALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHE
Retrocopy MATVPKLLQQQEEEHSKLRSVSVDLNVDPLLQTDISYALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHE

Parental  DFVWLHDTLIETTDYAGLIIPPAPAKPDFDGPREKMQKLGEGEGSMTKEE-AKMKQELEAEYLAVFKKTV
          DFVWLHDTLIETTDYAGLIIPPAPAKPDF.GP.EKMQKLGEGEG.MTKEE.AKMKQELEAEYL.VFKKTV
Retrocopy DFVWLHDTLIETTDYAGLIIPPAPAKPDFNGP*EKMQKLGEGEGFMTKEEFAKMKQELEAEYLMVFKKTV

Parental  SSHEVFLQRLSSHPVLSKDRNFHIFLEYDQDLSVRRKNTKEMFGGFFKSVVK-SADEVLFSGVKEVDDFF
          SS.EV.LQRLSSHPVLS.D.NFHIFLEYDQDLSVR.KNTKEMFGGFFKSV.K.S.DEVLFSGV.EVDDFF
Retrocopy SSREVSLQRLSSHPVLSNDCNFHIFLEYDQDLSVRQKNTKEMFGGFFKSVLK<STDEVLFSGVVEVDDFF

Parental  EQEKHFLSNYYDRIKGSCAKADRMTSAHKNVADDYIHTAACLHSLALEEPTVIKKYLLKAAELFEKLRKV
          EQE..FLSNYYDRIKGS.AKADRMTSA.KNVAD.YI.TAACLHSLALEEPTVI.KYLLK.AEL.EKLRKV
Retrocopy EQERYFLSNYYDRIKGSFAKADRMTSANKNVADGYILTAACLHSLALEEPTVIRKYLLKVAELSEKLRKV

Parental  ESRVSSDEDLKLTELLRYYMLNIEAAKDLLY-RTKALIDYENSN-ALDKARLKSKDVKLAEAHHHECCQK
          ESRVSSDEDLKLTELLRYYMLNIEAAKDLLY.RT.ALIDYENSN..LDKA.LKSKDVKLAEA...E.CQK
Retrocopy ESRVSSDEDLKLTELLRYYMLNIEAAKDLLYRRTEALIDYENSNKVLDKAWLKSKDVKLAEAYQQEYCQK

Parental  FEQLSESAK--LINFKRKRVAAFRKNLIEMSELEIKHARNNVSLLQSCIDLFKNN
          FEQLSESAK..LINFK.KRVAAFRKNLIEMSELEIKHARNN.S.LQSCIDLFKNN
Retrocopy FEQLSESAKEELINFKQKRVAAFRKNLIEMSELEIKHARNNISFLQSCIDLFKNN

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_410 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_410 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478, retro_chof_2166,
Callithrix jacchus	ENSCJAG00000004947	2 retrocopies	retro_cjac_2192, retro_cjac_3243,
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746, retro_mmul_832,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071,
Oryctolagus cuniculus	ENSOCUG00000017072	1 retrocopy	retro_ocun_1323,
Otolemur garnettii	ENSOGAG00000006157	1 retrocopy	retro_ogar_1203,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052, retro_ptro_717,
Sus scrofa	ENSSSCG00000007088	1 retrocopy	retro_sscr_593,
Ictidomys tridecemlineatus	ENSSTOG00000015416	1 retrocopy	retro_itri_1176,
Tursiops truncatus	ENSTTRG00000016432	1 retrocopy	retro_ttru_410 ,