RetrogeneDB ID: retro_ttru_6

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1196:445839..446967(-)
• Located in intron of: ENSTTRG00000013156

Retrocopy information

• Ensembl ID: ENSTTRG00000013157
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RNF128
• Ensembl ID: ENSTTRG00000007536
• Aliases: None
• Description: ring finger protein 128, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21153]

Sequence

>retro_ttru_6
ATGCATCTACTCAAGATTGGCACTCGGAGAAACAGCACTGCCTCTTCCTGGCTCATGAAATTCAGTTTCCTTTGGCTGCT
TAGCCAGCACTGTTGCAGAGCCAGAGCTGTTTGGACTGCATACACGAACATATCATTTCACGTTGGGAATCGCATGTTGT
CAGAGTTGGGGGAGACTGGAGTGTTTGGAAGAAGCTCTGCTCTCAAGAGAGTGGCGGGAGTTATCGTGCCTCCAGAGGGA
AAAACGCAAAACGCATGTGACCCCGGTACCAGTTTCAGCACATCGAAGAACTCGGAGACGTGGCTCGCACTTGTTGAACG
GGGAGGCTGTACCTTCACACAGAAGATCAAGGTGGCCGTGGAGAAGGGAGCCAGCGGAGTGATCATCTATAACTTCCTAG
GAACTGGCAATCGGGTTTTTCCCATGTCTCATCAGGCGTTTAAAGACATCGTCGTGGTGATGATTGGTAACTTGAAAGGC
ATGGAGATTTTGCATTTAATTCAGAAGGGAGTTCACGTTACAGTCATGATTGAGGTGGGAAGAAAACACATCATCTGGAT
GAATCACTATTTTGTCTCTTTTGTGATTGTCACAACCGCTCCGCTAGCGTATTTCATCTTTTATCATATTCAAAGACTTT
GGGTAGCAAGGATTCAGAACAGGAGATGGCAGCGGTTAACAAGTGATCTCAAGAAAGCATGTGGCCAGCTTCAACTTCGG
GTACTTAAAGAGGGGGACAAGGAAGTAAGTCCAAATGGAGATAGCTGTGTAGTTTGCTTTGAACTCTATAAGCCTAATGA
TACAGTTCGTATTCTGACTTGTAAACATTTTTTCCACAAGAACTGCATTGACCCCTGGATTCTAGCCCGTGGGACATGCC
CCATGTGCAAATGTGACATTCTTAAAGCTTTGGGGATTCAGGTGGATGTTGAAGATGGAACAGAATCTGTGCAAGTTCTA
ATGTTGAATGAATTGCCTGGTATCCTGTCACCTCGTGAAGAGGGCACAAGTAATGAACTTCCTCCTGCGGGAAGGTCAAA
TAAAGGGACGCACGTGGAGGAGTGCCCTACTTGTCAGAACGATGGCCCGTCTAATTCAGTAGCAGCAAACGTTCATCGTC
CACCTTGA

Alignment

ORF - retro_ttru_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.37 %
• Parental protein coverage: 58.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQSIQ
          .WLAL..RGG.CTF..KI..A.E.GASG..I.NF.GT.N.V.PMSH....DIV..MIGNLKG..IL..IQ
Retrocopy TWLALVERGG-CTFTQKIKVAVEKGASGVIIYNFLGTGNRVFPMSHQAFKDIVVVMIGNLKGMEILHLIQ

Parental  RGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
          .G..VT..IEVG.KH..W.NHY...FV.V.....TA...........R.L..AR.Q.R....L..D.KKA
Retrocopy KGVHVTVMIEVGRKHIIWMNHYFVSFVIVT----TAPLAYFIFYHIQR-LWVARIQNRRWQRLTSDLKKA

Parental  IGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHIFHKTCVDPWLLEHRTCPMCKCDILKA
          .G.LQLR.LK.GDKE..P.GDSC.VC.ELYKPND.VRILTC.H.FHK.C.DPW.L...TCPMCKCDILKA
Retrocopy CGQLQLRVLKEGDKEVSPNGDSCVVCFELYKPNDTVRILTCKHFFHKNCIDPWILARGTCPMCKCDILKA

Parental  LGIEVDVEDGSVSLQVPASNEASNSASPHEEDNRSETASSG
          LGI.VDVEDG..S.QV...NE.....SP.EE....E....G
Retrocopy LGIQVDVEDGTESVQVLMLNELPGILSPREEGTSNELPPAG

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_6 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_6 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022920	1 retrocopy	retro_btau_1358,
Loxodonta africana	ENSLAFG00000002816	1 retrocopy	retro_lafr_946,
Macropus eugenii	ENSMEUG00000001567	1 retrocopy	retro_meug_1139,
Mustela putorius furo	ENSMPUG00000003695	1 retrocopy	retro_mputfur_340,
Oryctolagus cuniculus	ENSOCUG00000012328	1 retrocopy	retro_ocun_37,
Pelodiscus sinensis	ENSPSIG00000010727	1 retrocopy	retro_psin_49,
Pan troglodytes	ENSPTRG00000022151	1 retrocopy	retro_ptro_2651,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Ictidomys tridecemlineatus	ENSSTOG00000022922	2 retrocopies	retro_itri_1254, retro_itri_1255,
Tursiops truncatus	ENSTTRG00000001298	1 retrocopy	retro_ttru_1062,
Tursiops truncatus	ENSTTRG00000007536	1 retrocopy	retro_ttru_6 ,
Tursiops truncatus	ENSTTRG00000016450	1 retrocopy	retro_ttru_351,