RetrogeneDB ID: retro_ttru_208

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1556:76057..76642(+)
• Located in intron of: ENSTTRG00000002954

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM5
• Ensembl ID: ENSTTRG00000010653
• Aliases: None
• Description: phosphoglycerate mutase family member 5 [Source:HGNC Symbol;Acc:28763]

Sequence

>retro_ttru_208
GGTTCCGCCACCTCGCTCTCCTGGGCTGTGGCCCCGGGGGTACTCGGAGCTGCACGTGGCCCAGCCTCCCGCGGGGTTGG
GAGCGGGGCTGGGCGGTGGAGTCCCGCCCCGGGCCTGGCGTCCAGGGCCCCACCTGGGAGAGGTGAGCAACACTAGCCTT
GCTCAACCTGTGGAAGAAGAGCCTGCAATCTGGAGAAGAACTAGTGTTCAGTCTGGACCACTACGAAGCCAAGGCCACGC
GGCACATCTTCCTCATCAGACACTCCCAGTACCACGCGAACGTCTCCCTGGAAAGAACCGCCCTTTGACCCCACGAGTCG
TGAACCGGAAGTACTAACTGGCCTGGGACTCACCAAGCTCGGAGTTGAAGTTTAATAAAATCGTCCGTCCGTCTGTGACC
AGCGCTATAGAAACCTCCAACAGCATCAGCTAACACCTGCCAGGCGTCTGGAAATTCAGCACAGTCCTGCTGGGGGGAAG
GCGGGCCCGTTGAAGCCGACCCGCCCGGGTCTCGCGGGAAACGGAGGCTGTGCGGAATCACGAGACTGAGCTCGGATGCA
GGCCGCCTTCTGGAACTGCATACAT

Alignment

ORF - retro_ttru_208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.88 %
• Parental protein coverage: 82.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GSAAVFFSAVAVGKPRAGGDAEPRVVEPPA-WAGAARPGPGVWDPNWDRREPLSLVNLRKRNLEPGEEEL
          GSA.....AVA.G...A......R.V...A.WA...RPGPGV..P.W.R...L.L.NL.K..L..GEE.L
Retrocopy GSATSLSWAVAPGVLGAARGPASRGVGSGA<WAVESRPGPGVQGPTWER*ATLALLNLWKKSLQSGEE-L

Parental  ASRLDHYKAKATRHIFLIRHSQYHVDASLE-KDRTLT-PLGREQAELTGLRLASLG-MKFNKIVHSSMTR
          ...LDHY.AKATRHIFLIRHSQYH...SLE.K.R.LT.P..RE...LTGL.L..LG..KFNKIV..S.T.
Retrocopy VFSLDHYEAKATRHIFLIRHSQYHANVSLE<KNRPLT<PTSREPEVLTGLGLTKLG>LKFNKIVRPSVTS

Parental  AIETTDIISKHLPGVCKVSTDLM-REGAPIEPDPPVSHWK-PEAVQYYE-DGARIEAAFRNYIH
          AIET...IS.HLPGV.K.ST.L...EG.P.E.DPP.S..K..EAV...E.D.AR..AAF.N.IH
Retrocopy AIETSNSIS*HLPGVWKFSTVLL>GEGGPVEADPPGSRGK<TEAVRNHE<D*ARMQAAFWNCIH

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_208 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_208 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052, retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762, retro_chof_2590,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208 ,