RetrogeneDB ID: retro_ttru_1321

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_110408:43447..44435(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACCSL
• Ensembl ID: ENSTTRG00000002727
• Aliases: None
• Description: 1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like [Source:HGNC Symbol;Acc:34391]

Sequence

>retro_ttru_1321
CAATGGAGTGATTTTGAAGCTGCATTTGCCAGCCATGACCTATTCAACTGTGGGATTGACATCTCTGCCTTGTACCATTC
CAGCTTCTAGGGCTACAAGAACTGCCATGGAGACAAATACCATGAGGACAAGAACACTTTGGGTTTCATTAATCTTGGTA
CCAGTGAGAATAAGCTGTGCTTTGATCTGATTACTGAAATTTTGAATCACAGTGACATGAACTGCATTGAGGAGATCCTG
CTGCAATATCCTGATTAGAGAGGGCAACCATCCCTGGGAAGAAGTGGGCTCGTTCCTGACCTACTACTGCAAGACACCTG
CCCACCTGGATCCAGAAAACTTGGTTGTTCTAAATGGCTGCCACTCTGTCTTCTCCGTGCTGACCATGGTTCTGTGCGAT
TCAGGTGAGGCCTTTCTGAGCCCTCACCACCTTCTATGGTGGCTTCCTCTTCAGCTCCCATCGGTATGTGAAAGTTGAGC
TGATGCTTGTCCACCCAGACAGTGAGATCACCAGTGTGAACATCCATCCTTTCCAGCTCAAGTGTAGAAGGTGGAGCAAG
CCCCACTTGAGGCTATGCTTAAGGGCAGTAAGGTCAGAGACCTTGTGTTAATTAACCCTCAGAATCCTCTGGGTGACCTC
TACTCCTGGGACTCACTGAAGGAATACCTAGAACTTGCCAAGCGGTGCAACCTACGTGTCATTATAGATGAGATTTACAT
GCTATCTGTGTTGGATGAATACATGATATTTCACAGTGTTCTGGGCATGGAAAGTTTGCCTGGTTTCAACAGGGCCCATG
TGATCTGAAGCACCAGTAAGGATTTTATCATTTCTGGCTTCTACTTTGGCACTCTGTATACCCACAACAAGGAGGTGGGC
TCTGCTGTGAGCTCCTCTGGCTGCCTCTGCAGCGTTTCTGGCATCACCCAGCACAAACTGTGTTGGCTACTCCAGGACAG
AGAACAGATTGACAAAGTGTATCCACCT

Alignment

ORF - retro_ttru_1321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.97 %
• Parental protein coverage: 65.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QRSDFEDTLIGYDLYNRGIDISALYHSSFQDY-TYQGNKYHKDENTLGYINLGTSE-KICIDLLAERLTR
          Q.SDFE......DL.N.GIDISALYHSSF..Y....G.KYH.D.NTLG.INLGTSE.K.C.DL..E.L..
Retrocopy QWSDFEAAFASHDLFNCGIDISALYHSSF*GYKNCHGDKYHEDKNTLGFINLGTSENKLCFDLITEILNH

Parental  TDMLYIDEDLLQYPDWRGQPFL-RKEVAR-FLTSDCKAPAHLDPENVVVLNGCSSVFSALAMVLCDPGEA
          .DM..I.E.LLQYPD.RGQP.L..K..AR.FLT..CK.PAHLDPEN.VVLNGC.SVFS.L.MVLCD.GEA
Retrocopy SDMNCIEEILLQYPD*RGQPSL<GKKWAR<FLTYYCKTPAHLDPENLVVLNGCHSVFSVLTMVLCDSGEA

Parental  FLVP-TPSYGGFIFSTHLYAKVELVPVHLESQVTEASAYPFQL-TVDKLERALLGAKIEGKKVRGLVLIN
          FL.P.T..YGGF.FS.H.Y.KVEL..VH..S..T.....PFQL..V.K.E.A.L.A...G.KVR.LVLIN
Retrocopy FLSP>TTFYGGFLFSSHRYVKVELMLVHPDSEITSVNIHPFQL<QV*KVEQAPLEAMLKGSKVRDLVLIN

Parental  HQNPLGDIYSRDSVMEYLEFAKKYNLHVIIDEIYMLSVFDEAIPFHSVLSLESLPDPNKTHVIWGTSKGF
          .QNPLGD.YS.DS..EYLE.AK..NL.VIIDEIYMLSV.DE...FHSVL..ESLP..N..HVI..TSK.F
Retrocopy PQNPLGDLYSWDSLKEYLELAKRCNLRVIIDEIYMLSVLDEYMIFHSVLGMESLPGFNRAHVI*STSKDF

Parental  GISGFRFGTLYTRNREVASAVSSFGYVHSISGVTQYKLCQLLQDREWVDNVYLP
          .ISGF.FGTLYT.N.EV.SAVSS.G...S.SG.TQ.KLC.LLQDRE..D.VY.P
Retrocopy IISGFYFGTLYTHNKEVGSAVSSSGCLCSVSGITQHKLCWLLQDREQIDKVYPP

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_1321 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1321 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011384	1 retrocopy	retro_cjac_100,
Dipodomys ordii	ENSDORG00000005058	1 retrocopy	retro_dord_340,
Equus caballus	ENSECAG00000011908	1 retrocopy	retro_ecab_575,
Echinops telfairi	ENSETEG00000009026	2 retrocopies	retro_etel_1006, retro_etel_204,
Homo sapiens	ENSG00000205126	1 retrocopy	retro_hsap_3553,
Myotis lucifugus	ENSMLUG00000005151	1 retrocopy	retro_mluc_1235,
Nomascus leucogenys	ENSNLEG00000017966	1 retrocopy	retro_nleu_2326,
Ochotona princeps	ENSOPRG00000002097	1 retrocopy	retro_opri_526,
Ochotona princeps	ENSOPRG00000006805	7 retrocopies	retro_opri_1064, retro_opri_1151, retro_opri_251, retro_opri_252, retro_opri_398, retro_opri_399, retro_opri_808,
Pongo abelii	ENSPPYG00000003340	1 retrocopy	retro_pabe_2934,
Pan troglodytes	ENSPTRG00000028662	1 retrocopy	retro_ptro_2414,
Tupaia belangeri	ENSTBEG00000016623	1 retrocopy	retro_tbel_3677,
Tursiops truncatus	ENSTTRG00000002727	1 retrocopy	retro_ttru_1321 ,