RetrogeneDB ID: retro_ttru_862

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_399:48785..49539(-)
• Located in intron of: ENSTTRG00000009563

Retrocopy information

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

Parental gene information

• Parental gene symbol: C4orf27
• Ensembl ID: ENSTTRG00000009751
• Aliases: None
• Description: chromosome 4 open reading frame 27 [Source:HGNC Symbol;Acc:26051]

Sequence

>retro_ttru_862
AAGTATAAAATGAACAAAAAATCAGCAAGCCCAATATTAACCTTCACTGGAGATTTTACTATGACCCTCCTGAGTTCCAG
ACTGTTATTACTGGAGATAATAAAATTCAGTTCCATGTGGGGTATTTCAGGGAGTCTCCTGATGAACCTCCTGTATATGT
TGGTACAGATGGAGCAAAGAAAAATTGTATAATTGATCAAAATGGAGATAATGTGTTTGCCGCAGTCAAATTTGTTTTGA
TGAAAAACTTAAGTAACATAAAAAGAAAACTAGTCTCTTGAAAAACATAGATGAAAACTGCACAGAAGCAGCCAGAGCAC
TGGGTTACTCATTGGAACAGAGAACCATGAAGATGAAACATAGAGATAAGAAAGTCAAGACAAAGACTTTTCATGATGCA
GGCTTAGTTGTCCCAGTAGATGAAAATGATGCTGAGTACGGAGAGCTCCCTGAAACGGATGCCAACTTCAAGGGAATTTG
CAAGACAATTTTTGAAGCACAAAGTGATGAGAGACTAAAAGCTTTTGCTCTCATTCAGCGATGACTTTTGTGCAGTTTGC
TAGTGATGAATGTGATTATGGGATGGGGCGTAAGTGGGAATGGACTTCCTTGTTATGGTTCAGACTATTGTCATAAAGTT
ACCTGCCAACTTTTACCTCTTACCTATACTCTGTTGAAGAGAAGTCTCTTTGCAGAAATTATTGAAGATTTTCTGGTAAA
CAGGAGTAAAGAAAACACAGACCAACTTGCAGCA

Alignment

ORF - retro_ttru_862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.23 %
• Parental protein coverage: 74.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RHKMKKKSASL-NFNLHWRFYYDPPEFQTIIIGDRKTEFHMGYFRDSPDELPVFVATNEAKKNCIIVQNG
          ..KM.KKSAS..N.NLHWRFYYDPPEFQT.I.GD.K..FH.GYFR.SPDE.PV.V.T..AKKNCII.QNG
Retrocopy KYKMNKKSASP<NINLHWRFYYDPPEFQTVITGDNKIQFHVGYFRESPDEPPVYVGTDGAKKNCIIDQNG

Parental  DNVFAAVKLFLM-KKLKEVTDKKKTSLLKTIDEKLTEAARELGFSLEQRTVKMKQRDKKVVTKTFHGAGL
          DNVFAAVK..LM..KLK....KKKTSLLK.IDE..TEAAR.LG.SLEQRT.KMK.RDKKV.TKTFH.AGL
Retrocopy DNVFAAVKFVLM<EKLK*--HKKKTSLLKNIDENCTEAARALGYSLEQRTMKMKHRDKKVKTKTFHDAGL

Parental  VVPVDKNDVGYRELPETDASLRRICKTIVEAPSDAERL-KAFAPVQEMMTYVQFANDECDYGMGLE-LGM
          VVPVD.ND..Y.ELPETDA....ICKTI.EA.SD.ERL.K.F......MT.VQFA.DECDYGMG....GM
Retrocopy VVPVDENDAEYGELPETDANFKGICKTIFEAQSD-ERL<KSFCS-HSAMTFVQFASDECDYGMGRK<VGM

Parental  DLF-CHGSHYFHKVAGQLLPLAYNLLKRNLFAEIIEAHLANRSREDVDQLAA
          D...C.GS.Y.HKV..QLLPL.Y.LLKR.LFAEIIE..L.NRS.E..DQLAA
Retrocopy DFL<CYGSDYCHKVTCQLLPLTYTLLKRSLFAEIIEDFLVNRSKENTDQLAA

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_862 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_862 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020132	1 retrocopy	retro_btau_611,
Equus caballus	ENSECAG00000013735	1 retrocopy	retro_ecab_551,
Gorilla gorilla	ENSGGOG00000003090	1 retrocopy	retro_ggor_2306,
Myotis lucifugus	ENSMLUG00000017052	1 retrocopy	retro_mluc_395,
Ictidomys tridecemlineatus	ENSSTOG00000001481	1 retrocopy	retro_itri_101,
Tursiops truncatus	ENSTTRG00000009751	1 retrocopy	retro_ttru_862 ,