RetrogeneDB ID: retro_ttru_736

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3204:310099..310573(-)
• Located in intron of: ENSTTRG00000011826

Retrocopy information

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

Parental gene information

• Parental gene symbol: PROSC
• Ensembl ID: ENSTTRG00000016940
• Aliases: None
• Description: proline synthetase co-transcribed homolog (bacterial) [Source:HGNC Symbol;Acc:9457]

Sequence

>retro_ttru_736
ATGTGGAGCGCTGGCAGCAAGCCACGGAGCTGTGGGATGGGTTCGCCCTGAGGGCAGTGAACAAGCGCGTGCAGCAGGGG
GGTAGCGCGGCAGCTGCGGGAACTCCCAGCCATCCAGCCCCAGCTAGTAGCAGTCAGCAAAACCAAACCTGCAGACATGG
GGATCGAGGCCTACAGTCACCAGCAGCGCACTTTCAGGGAGAGCTATGTTCAGGAACTGCTTGAAAAAGCATCAAATCCT
AAAATTCTGTCTTCATGTCCTGAGATCAAATGGCACTTCATTGGCCATCTACAGAAACAAAATGTCAGCAGATTGATGGC
TGTCCCCACTCTCTTCATGCTGGAAACAGTGGATTCTGTGAAGCTGGCAGACAAAGTGAGCAGTGCGTGGCAGGAAAAAG
GTTCTCCCGAAAGGTAAAAGGTTATGGACCAGATTAACACCAGCGGAGAGGAGAGCAAACGTGGCCTGCCCCCA

Alignment

ORF - retro_ttru_736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 57.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MWRAGS-MSAELGVGFALRAVNERVQQA-VTRRPRELPAIQPRLVAVSKTKPADMVIEAYSHGQRTFGEN
          MW.AGS....EL..GFALRAVN.RVQQ..V.R..RELPAIQP.LVAVSKTKPADM.IEAYSH.QRTF.E.
Retrocopy MWSAGS<QATELWDGFALRAVNKRVQQG>VARQLRELPAIQPQLVAVSKTKPADMGIEAYSHQQRTFRES

Parental  YVQELLEKASNPKILSSCPEIKWHFIGHLQKQNVNKLMAVPNLFMLETVDSVKLADKVNSAWQKKGSPER
          YVQELLEKASNPKILSSCPEIKWHFIGHLQKQNV..LMAVP.LFMLETVDSVKLADKV.SAWQ.KGSPER
Retrocopy YVQELLEKASNPKILSSCPEIKWHFIGHLQKQNVSRLMAVPTLFMLETVDSVKLADKVSSAWQEKGSPER

Parental  LKVMVQINTSGEESKHGLPP
          .KVM.QINTSGEESK.GLPP
Retrocopy *KVMDQINTSGEESKRGLPP

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_736 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_736 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006193	1 retrocopy	retro_cfam_1974,
Sus scrofa	ENSSSCG00000015826	1 retrocopy	retro_sscr_347,
Tursiops truncatus	ENSTTRG00000016940	1 retrocopy	retro_ttru_736 ,