RetrogeneDB ID: retro_ttru_1175

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_106406:95383..95872(+)
• 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_1175
TTTGGTGCTGGCAGTACAAGTACCGGTGGCGGGGATGCTAACAGCGTCCGCCTGGCCCCCTCCACGATGTCCAAGGCCGA
GGAGGCCCGGAAGCTGGCAGGCTGCGCGGCCGTGGAGAATCACTTGAGGAATAACCAAGTGCTGGGAATTGGGAGTGGTT
CTACAATTGTCCATGCTGTGCAGCAAATAGCTGAAAGAGTGAAACAAGAGAATCTGAATCTCGTCTGTATTCCCACTTCC
TTCCACGCCCATCAGCTCATCCTGCAGTATGGCTGAACTCTCGGTGACCTGGACCGACGACCAGAGATTGACCTTGCCAT
CGATGGTGCTGATGCAGTAGATGCTGATTTCAATCTCGTCAAGGGTGGTGGAGGCTGCCTGACCCAGGAGAAAATTGTGG
CTGGCAACGCCAGTTGCTTCATCGTGATTGCCAGTTTCCGGAAAGATTCAAAGAACCTCGGGGATCAGTGGCACAAGGTC
ATCCCGATG

Alignment

ORF - retro_ttru_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.73 %
• Parental protein coverage: 52.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FGTGSTSTAGGDANSVCPAPSTMSKAEEAKKLAGRAAVENHVRNNQVLGIGSGSTIVHAVQRIAERVKQE
          FG.GSTST.GGDANSV..APSTMSKAEEA.KLAG.AAVENH.RNNQVLGIGSGSTIVHAVQ.IAERVKQE
Retrocopy FGAGSTSTGGGDANSVRLAPSTMSKAEEARKLAGCAAVENHLRNNQVLGIGSGSTIVHAVQQIAERVKQE

Parental  NLNLVCIPTSFQARQLILQYGLTLSDLDRHPEIDLAIDGADEVDADLNLIKGGGGCLTQEKIVAGNASRF
          NLNLVCIPTSF.A.QLILQYG.TL.DLDR.PEIDLAIDGAD.VDAD.NL.KGGGGCLTQEKIVAGNAS.F
Retrocopy NLNLVCIPTSFHAHQLILQYG*TLGDLDRRPEIDLAIDGADAVDADFNLVKGGGGCLTQEKIVAGNASCF

Parental  IVIADFRKDSKNLGDQWHKGIPI
          IVIA.FRKDSKNLGDQWHK.IP.
Retrocopy IVIASFRKDSKNLGDQWHKVIPM

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_1175 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1175 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,