RetrogeneDB ID: retro_ttru_854

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_374:68777..70090(-)
• Located in intron of: ENSTTRG00000006610

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT13
• Ensembl ID: ENSTTRG00000002506
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13) [Source:HGNC Symbol;Acc:23242]

Sequence

>retro_ttru_854
ACGAGTGTGGTGATTGTTTCCCACAATGAGGCTTGGAGCACACTTCTGCGAACTGTCCATAGTGTCATTAATCGCTCACC
AAGACACATGGGAGATGAAATTGTTCTAGTAGATGAGGCCAGTGAAAGAGACTTTTTGAAAAGACCTCTAGAGAGTTATG
TGAAAAAATTAAATTACCAGTTCATGTCATTCGAATGAAGCCATGCTCTGGATTGATCAGAGCTAGGTTAAAAGGAGCTG
CAGTGTCTAAAGGCCAAGTGATCACCTTTTAAGATGCTCACTGTGAGTGTACAGTGGGGTGGCTGGAGCCTCTCTTAGCC
AGGATCAAACATGACAGGAAGACAGTGGACTATCCTATCATTGATGTGATCAGTGATGATACTTTTGAGTACAAGGCGGG
TTCTGACATGACCTATGGCGGATTCAACTGGAAGCTTAATTTTCGCTGGTATCCTGTTCCCCAAAGAGAAATGGACAGAA
GGAAAGGTGATTGAATTCTTCCTGTGAGAACACCTACAATGGCAGGAGGCCTTTTTTCAATAGACAGAGATTACTTTCAG
GAAATTGGAACATATGATGCTGGAATGGATATTTGGGGAGGAGAAAACCTAGAAATTTCCTTTAGGATTTGGCAGTGTGG
AGGAACTTTGGAGATTGTTACTTGCTCACATGTTGGACATGTGTTTCAGAAAGCTACACCCTACACGTTTCCAGGAGGCA
CAGGGCAGATTATCAATAAAAATAACAGATGACTTGCAGAAGTGTGTATGGATGAATTCAAGCATTTCTTCTATATAATT
TATCCAGGTGTTACAAAGGTAGATTATGGAGATATATCACCAAGACTTGGTCTAAGACGCAAACCCCAATGCAGACCTTT
CTTTTGGTACCTAGAGAATATTTATGCAGATTCTCAGATTCCACATCACTATTTCTCTTTGGGAGAGATACGAAATGTGG
AAACAAATCAGTGTCTGGATAACATGGCTAGAAAAGAGAATGAAAAAGCTGGAATTTTTAACTGTCATGGTATGGGAGGT
AATCAGGTTTTCTCTTACACTGCCAACAAAGAAATTAGAACAGATGACCTTTGCTTGGGTGTCTCCAAACTTAATGGCCC
AGTCACAATGCTCAAATGCTACCACCTAAAAGGCAACCAACTTTGGAAGTATGACCCGGTGAAATTAACCCTGCAGCCTG
CGAACAGTAATCAGTGCCTAGATAAAGCCACAGAAGAGGATAGCCAGGTGTCCAGCATTAGAGACTGCAATGGAAGCCAG
TCCTAGCAGTGGCTTCTTTGAAATGTCACCCTT

Alignment

ORF - retro_ttru_854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.73 %
• Parental protein coverage: 78.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSVVIVFHNEAWSTLLRTVYSVINRSPHYLLSEVILVDDASERDFLKLTLDNYVKNL-EVPVKIIRMEER
          TSVVIV.HNEAWSTLLRTV.SVINRSP.....E..LVD.ASERDFLK..L..YVK.L...PV..IRM...
Retrocopy TSVVIVSHNEAWSTLLRTVHSVINRSPRHMGDEIVLVDEASERDFLKRPLESYVKKL<KLPVHVIRMKPC

Parental  SGLIRARLRGAAASKGQVITFLDAHCECTLGWLEPLLARIKEDRKTVVCPIIDVISDDTFEYMAGSDMTY
          SGLIRARL.GAA.SKGQVITF.DAHCECT.GWLEPLLARIK.DRKTV..PIIDVISDDTFEY.AGSDMTY
Retrocopy SGLIRARLKGAAVSKGQVITF*DAHCECTVGWLEPLLARIKHDRKTVDYPIIDVISDDTFEYKAGSDMTY

Parental  GGFNWKLNFRWYPVPQREMDRRKGDRTLPVRTPTMAGGLFSIDRNYFEEIGTYDAGMDIWGGENLEMSFR
          GGFNWKLNFRWYPVPQREMDRRKGD..LPVRTPTMAGGLFSIDR.YF.EIGTYDAGMDIWGGENLE.SFR
Retrocopy GGFNWKLNFRWYPVPQREMDRRKGD*ILPVRTPTMAGGLFSIDRDYFQEIGTYDAGMDIWGGENLEISFR

Parental  IWQCGGSLEIVTCSHVGHVFRKATPYTFPGGTGHVINKNNRRLAEVWMDEFKDFFYIISPGVVKVDYGDV
          IWQCGG.LEIVTCSHVGHVF.KATPYTFPGGTG..INKNNR.LAEV.MDEFK.FFYII.PGV.KVDYGD.
Retrocopy IWQCGGTLEIVTCSHVGHVFQKATPYTFPGGTGQIINKNNR*LAEVCMDEFKHFFYIIYPGVTKVDYGDI

Parental  SVRRTLRENLKCKPFSWYLENIYPDSQIPRRYYSLGEIRNVETNQCLDNMGRKENEKVGIFNCHGMGGNQ
          S.R..LR....C.PF.WYLENIY.DSQIP..Y.SLGEIRNVETNQCLDNM.RKENEK.GIFNCHGMGGNQ
Retrocopy SPRLGLRRKPQCRPFFWYLENIYADSQIPHHYFSLGEIRNVETNQCLDNMARKENEKAGIFNCHGMGGNQ

Parental  VFSYTADKEIRTDDLCLDVSRLNGPVIMLKCHHMRGNQLWEYDAERLTLRHVNSNQCLDEPSEEDKMVPT
          VFSYTA.KEIRTDDLCL.VS.LNGPV.MLKC.H..GNQLW.YD...LTL...NSNQCLD...EED..V..
Retrocopy VFSYTANKEIRTDDLCLGVSKLNGPVTMLKCYHLKGNQLWKYDPVKLTLQPANSNQCLDKATEEDSQVSS

Parental  MQDCSGSRSQQWLLRNMTL
          ..DC.GS.S.QWLL.N.TL
Retrocopy IRDCNGSQS*QWLL*NVTL

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_854 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_854 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013917	1 retrocopy	retro_mmur_228,
Oryctolagus cuniculus	ENSOCUG00000017645	1 retrocopy	retro_ocun_274,
Otolemur garnettii	ENSOGAG00000016208	2 retrocopies	retro_ogar_2525, retro_ogar_3272,
Tupaia belangeri	ENSTBEG00000000869	1 retrocopy	retro_tbel_1671,
Tursiops truncatus	ENSTTRG00000002506	2 retrocopies	retro_ttru_793, retro_ttru_854 ,
Tursiops truncatus	ENSTTRG00000010848	1 retrocopy	retro_ttru_212,
Tursiops truncatus	ENSTTRG00000017058	1 retrocopy	retro_ttru_1819,