RetrogeneDB ID: retro_ttru_1887

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_97285:45987..47120(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NCL
• Ensembl ID: ENSTTRG00000009094
• Aliases: None
• Description: nucleolin [Source:HGNC Symbol;Acc:7667]

Sequence

>retro_ttru_1887
CTTGTCAAAGAAGCACCTGGAAAACGAAAGAAGGAAATGGCCAAACAAGAAGCAGCTCCTGAAGCCAAGAAACAGAAAGT
GGAAGCCACAGAACCAACTACATCTTTCAATCTCTTTGTTGGAAACCTGAACTTCAGTAAATCTGCTCCTGAATTGAAAA
CGGGTATCAGTGACATTTTTGCTAAAAATGGTCTTGCAGTTGTTGATGGCAGAATTGGTGTGTCTAGGAAGTTTGGCTAC
GTGGATTTTGAATCTGCTGAAGACCTGGAAAAAGCCTTGGAACTCACTGGTTTAAAAGTCTTTGGCAATGAAATTAAACT
AGAAAAATCAAAGGGAAAAGACAGTAAGAAAGATTGAGATGCGAGAACACTTTTGGCTAAAAATCTGTCTTATAAAGTTA
CTTAGGAAGAATTAAAAGAAGTGTTTGAAGATGCTGTGGATATCAGATTAGTCAGCAGGGATGGAAAGAATAAAGGGATT
GCTTACATTGAATTTAAGACAGAAGCTGATGCAGAGAAAACCTTGGAAGAAAAGCAGGGAACAGAGATAGATGGGCGATC
CATTTCCCTGTACTATACCAGAGAGAAAGGTCAAAGTCAAGACTATAGAGGTGGAAAGAATAGCATTGGAGTGGTGAATC
AAAAACCCTGGTTTTAAGCAACCTCTCCTGTAGTGCAACGGAAGAAACTCTTCAGGAAGTATTTGAGAAGGCAACATTTA
TCAAAGTGCCCCAGAACCAAAATGGCAAATCGAAAGGGTATGCATTTATAGAATTTGCTTCATTTGAAGATGCTAAAGAA
GCTTTAAATTCATGTAATAAAAGGGAAATTGAGGGCAGAGCCATCAGGCTGGAGTTGCGAGGACCCAGGGGATCACCTAA
TGCAAGAAGCTAGCTATCCAAAACTCTGTTTGTCAAAGGTCTATCTGAGGATACTACAGAAGAGACATTAAAGGAGTCGT
TCGACGGCTCTATTCGTGCAAGCGTAGTCACTGACCGGGAGGCTGGATCCTCCAAGGGGTTTGGTTTTGTAGACTTCAAC
AGTGAGGAAGATGCCAAAGCTGCCAAGGAGGCCATGGAAGATGGTGAAATTGATGGAAACATAGTTACTTTGGACTGGGC
CAAGCCTAAGGGT

Alignment

ORF - retro_ttru_1887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.08 %
• Parental protein coverage: 53.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVKEAPGKRKKEMAKQKAAPEAKKQKVEATEPTTSFNLFVGNLNFSKSAPELKTGISDLFAKNDLAVVDV
          LVKEAPGKRKKEMAKQ.AAPEAKKQKVEATEPTTSFNLFVGNLNFSKSAPELKTGISD.FAKN.LAVVD.
Retrocopy LVKEAPGKRKKEMAKQEAAPEAKKQKVEATEPTTSFNLFVGNLNFSKSAPELKTGISDIFAKNGLAVVDG

Parental  RIGVSRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQEELKE
          RIGVSRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK.KGKDSKK..DARTLLAKNL.YKVT.EELKE
Retrocopy RIGVSRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKSKGKDSKKD*DARTLLAKNLSYKVT*EELKE

Parental  VFEDAVEIRLVSKDGKSKGIAYIEFKTEADAEKTLEEKQGTEIDGRSISLYYTGEKGQGQDHRGGKNST-
          VFEDAV.IRLVS.DGK.KGIAYIEFKTEADAEKTLEEKQGTEIDGRSISLYYT.EKGQ.QD.RGGKNS..
Retrocopy VFEDAVDIRLVSRDGKNKGIAYIEFKTEADAEKTLEEKQGTEIDGRSISLYYTREKGQSQDYRGGKNSI<

Parental  WTGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQSGKSKGYAFIEFASFEDAKEALNSCNKREIEG
          W.GESKTLVLSNLS.SATEETLQEVFEKATFIKVPQNQ.GKSKGYAFIEFASFEDAKEALNSCNKREIEG
Retrocopy WSGESKTLVLSNLSCSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEG

Parental  RAIRLELQGPRGQPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSE
          RAIRLEL.GPRG.PNARS..SKTLFVKGLSEDTTEETLKESFDGS.RA..VTDRE.GSSKGFGFVDFNSE
Retrocopy RAIRLELRGPRGSPNARS*LSKTLFVKGLSEDTTEETLKESFDGSIRASVVTDREAGSSKGFGFVDFNSE

Parental  EEAKAAKEAMEDGEIDGNKVTLDWAKPKG
          E.AKAAKEAMEDGEIDGN.VTLDWAKPKG
Retrocopy EDAKAAKEAMEDGEIDGNIVTLDWAKPKG

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_1887 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1887 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016174	1 retrocopy	retro_btau_1713,
Myotis lucifugus	ENSMLUG00000014547	1 retrocopy	retro_mluc_685,
Otolemur garnettii	ENSOGAG00000027852	1 retrocopy	retro_ogar_1417,
Tursiops truncatus	ENSTTRG00000009094	2 retrocopies	retro_ttru_1887 , retro_ttru_51,