RetrogeneDB ID: retro_ttru_799

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3486:986..1575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPIA
• Ensembl ID: ENSTTRG00000000876
• Aliases: None
• Description: ribose 5-phosphate isomerase A [Source:HGNC Symbol;Acc:10297]

Sequence

>retro_ttru_799
ACAAGTACTGGTGGCGGGGACGCTAACAGCATCTGCCTGGCCCCCTCCGTCATGTCCAAGGCTGAGGAGGCCAAGAAGCT
GGCAGGCCGTGCAGCGGTGGAGAACCACGTGAGGAATAACCAAGTGCTGGGAATTGGGAATGGTTCTACAGTTGTCCACG
CCGTGCAGCAAATAGCTGAAAGGGTGAAACAAGAGAATCTGAACCCCGTCTGTATTCCCACTTCCTTCCAGGCCCGTCAG
CTCATCCTGCAGTTTGGCTGAACTCTTGGTGACCTGGACCGACACCCAGAGACTGACCTCACCATCGATGGTGCCGATGA
GGTAGATGTTGATCTCAATCTCATCAAGGGCAGTAGAGGATGCCTGACTCAGGAGAAAATTGTGGCTGGCAATGCCAGTT
GCTTCATCGCGATCACCGATTTCAGGAAAGGTTCAAAGAACCTCAGGGAATCAGTGGCACAAGGGGAACCCCCAACAAGG
TCATCCCGATGGCCTATTCCCAGTGAGCCGAGCTGTGACCCAGAAGTTTGGGGGCGTGATTGAACTTCGAATGGCCATCA
ACAAGGCAGATCCCTTGGTGATGGGTAAC

Alignment

ORF - retro_ttru_799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.42 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TSTAGGDANSVCPAPSTMSKAEEAKKLAGRAAVENHVRNNQVLGIGSGSTIVHAVQRIAERVKQENLNLV
          TST.GGDANS.C.APS.MSKAEEAKKLAGRAAVENHVRNNQVLGIG.GST.VHAVQ.IAERVKQENLN.V
Retrocopy TSTGGGDANSICLAPSVMSKAEEAKKLAGRAAVENHVRNNQVLGIGNGSTVVHAVQQIAERVKQENLNPV

Parental  CIPTSFQARQLILQYGLTLSDLDRHPEIDLAIDGADEVDADLNLIKGGGGCLTQEKIVAGNASRFIVIAD
          CIPTSFQARQLILQ.G.TL.DLDRHPE.DL.IDGADEVD.DLNLIKG..GCLTQEKIVAGNAS.FI.I.D
Retrocopy CIPTSFQARQLILQFG*TLGDLDRHPETDLTIDGADEVDVDLNLIKGSRGCLTQEKIVAGNASCFIAITD

Parental  FRKDSKNL-GDQWHK-GIPIEVIPMAY-VPVSRAVTQKFGGVIELRMAVNKAGPVVTDN
          FRK.SKNL.G.QWHK.G.P..VIPMAY..PVSRAVTQKFGGVIELRMA.NKA.P.V..N
Retrocopy FRKGSKNL>GNQWHK>GTPNKVIPMAY<FPVSRAVTQKFGGVIELRMAINKADPLVMGN

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_799 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_799 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002866	1 retrocopy	retro_btau_1373,
Equus caballus	ENSECAG00000011754	1 retrocopy	retro_ecab_645,
Macropus eugenii	ENSMEUG00000008256	1 retrocopy	retro_meug_1506,
Microcebus murinus	ENSMICG00000006462	1 retrocopy	retro_mmur_722,
Myotis lucifugus	ENSMLUG00000005384	1 retrocopy	retro_mluc_1129,
Monodelphis domestica	ENSMODG00000009649	1 retrocopy	retro_mdom_320,
Oryctolagus cuniculus	ENSOCUG00000006840	3 retrocopies	retro_ocun_1541, retro_ocun_1708, retro_ocun_1709,
Otolemur garnettii	ENSOGAG00000034178	2 retrocopies	retro_ogar_1218, retro_ogar_518,
Tarsius syrichta	ENSTSYG00000006406	8 retrocopies	retro_tsyr_1081, retro_tsyr_1088, retro_tsyr_1902, retro_tsyr_2028, retro_tsyr_393, retro_tsyr_709, retro_tsyr_725, retro_tsyr_994,
Tursiops truncatus	ENSTTRG00000000876	2 retrocopies	retro_ttru_1175, retro_ttru_799 ,