RetrogeneDB ID: retro_ttru_1894

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_97610:71..789(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PMM2
• Ensembl ID: ENSTTRG00000014827
• Aliases: None
• Description: phosphomannomutase 2 [Source:HGNC Symbol;Acc:9115]

Sequence

>retro_ttru_1894
CCCAGTGTCTGTTCCTTTGGTGTGGACTGGACCCTGCTGCCCCCTCAGCAGAAAATTACTAAGGAAATAAATGGCATTCT
ACAAAAATTGAGGCAGAAGATCAAAATCTGAGTCGTAGGCAGGTTGAATTTCAATAAAGTGCAGGTGAAGCTGGGAAATG
ATATGGTTAAAAAAATATGATTATGTGTTTCCAGGAAATGGCTTCGTAGCATACAAAGTTGGGCAACTCTTATATAAACA
GAATATTCAAGGTCACCTTGGTAAGGCCCTAATCCAAGATTTAATCAATGACTGTCTAAGCTACATTGTAGAAACCAAAC
TCCTGAAGAAGAAGGGTTGCTTTCATTGAAATTCTAAATGGGATGTGAATTCATCCTCTATTGAAAGAAGCTGCAGCCCC
AAAGAACACATGGAGTTCTATATGCATTATAAAGAAATAAAATATAAGACAAAAATGTGTAGCAGATCTGTGGAAAGCAT
TTGCAAATAAAGGCCTCACCTTTTCTGTAGGAGGCCAAATCAGTTTTGAGGTCTTTTGGGATGGATAGAGAAAGAGGTAT
TGCCTGGGACATGTGGAAAATCATGGTTATAAGACCATTTCTTTCTTTGGAGACAAAACTGTGGCAGGTGGGAACGACCA
TGAGATCTTCACAGACCTGGGAACTGCAGGCCACACGAGTCTGTGCCTGAGGACACAGGAAAGATCTGTGAAGAGCTC

Alignment

ORF - retro_ttru_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.16 %
• Parental protein coverage: 97.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PALCLFDVDGTLTAPRQKITKDMDCFLQKLRQKIKVGVVGGSDFEKVQEQLGNDVVEK-YDYVFPENGLV
          P..C.F.VD.TL..P.QKITK.....LQKLRQKIK..VVG...F.KVQ..LGND.V.K.YDYVFP.NG.V
Retrocopy PSVCSFGVDWTLLPPQQKITKEINGILQKLRQKIKI*VVGRLNFNKVQVKLGNDMVKK>YDYVFPGNGFV

Parental  AYKDGKLLCKQNIQGHLGEALIQDLINYCLSYISKIKLPKKRG-TFIEFRNGM-LNVSPVGRSCSQEERI
          AYK.G.LL.KQNIQGHLG.ALIQDLIN.CLSYI...KL.KK.G..FIE..NGM..N.S...RSCS..E..
Retrocopy AYKVGQLLYKQNIQGHLGKALIQDLINDCLSYIVETKLLKKKG>AFIEILNGM<VNSSSIERSCSPKEHM

Parental  EFYE-LDQKESIRQKFVEDLRREFAGKGLTFSIGGQISFDVFPDGWDKRYCLGHVEKDGYETIYFFGDKT
          EFY.....K..IRQK.V.DL...FA.KGLTFS.GGQISF.VF.DG..KRYCLGHVE..GY.TI.FFGDKT
Retrocopy EFYM>IIKK*NIRQKCVADLWKAFANKGLTFSVGGQISFEVFWDG*RKRYCLGHVENHGYKTISFFGDKT

Parental  MPGGNDHEIFTDPRTVGYT-VTAPEDTRRICEQL
          ..GGNDHEIFTD..T.G.T....PEDT..ICE.L
Retrocopy VAGGNDHEIFTDLGTAGHT<ESVPEDTGKICEEL

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_1894 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1894 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001440	2 retrocopies	retro_btau_1188, retro_btau_307,
Monodelphis domestica	ENSMODG00000005737	1 retrocopy	retro_mdom_285,
Otolemur garnettii	ENSOGAG00000016560	1 retrocopy	retro_ogar_1095,
Sus scrofa	ENSSSCG00000021236	1 retrocopy	retro_sscr_329,
Tursiops truncatus	ENSTTRG00000014827	2 retrocopies	retro_ttru_1894 , retro_ttru_977,