RetrogeneDB ID: retro_ttru_51

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1046:693067..694204(+)
• Located in intron of: ENSTTRG00000007887

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_51
GAACTTGTCAAAGAAGCACCTGGAAAGCGAACGAAGGAAATGGCCAAACAAAAAGCAGCTCCCGAAGCCAAGAAACAGAA
AGTGGAAGCTACAGAACCAACTACATCTTTCAATCTCTTTGTTGGAAACCTGAACTTCAGTAAATCTGCTCCTGAAATGA
AAACGGGTTTTAGTGACCTTTTTGCAAAAAATGATCTTGCAGTTGTTGATGTCAGAATTGGTGTGTCTAGGAAGTTTGGC
TATGTGGATTTTGAACCTGCTGAAGACCTGGAACAAGCCTTGGAACTCACTGGTTTAAAAGTCTTTGGCAATGAAATTAA
ACTAGAAAAACCAAAGGGGAAAGACAGTAAGAAAGAACAAGATGCGAGAACACTTTTGGCTAAAAATCTTCCTTATAAAG
TTACTCAGGAAGAATTAAAAGAAGTGTTTGAAGATACTGTGGAGATCAGATTAGTCAGCAAGGATGGAAAGTGTAAAGGG
ATTGCTTATATTGAATCTAGGACAGAAGCTGATGCAGAGAAAACCTTGGAAGAAAAACAGGGAACAGAGATAGATGGGCG
ATCCATTTCCCTGTACTATACTGGAGAGAAAGGTCAAAGTCAAGACTATAGAGGTGGAAAGAATAGCACTTGGACTGGTG
AATCAAAAACCCTGGTTTTAAGCAACCTCTCCTATAGTGCAATGGAAGAAACTCTTCAGGAAGTATTTGAGAAGGCAACG
TTTATCAAAGTGCCCCAGAATCAAAATGGCAAATCTAAAGGGTATGCATTTATAGAATTTGCATCATTTGAAGATGCTAA
AGAAGCTTTAAATTCATGTAATAAAAGGGAAATTGAGGGCAGAGCCATAAGGCTGGAGTTGCAAGGACCCAGGGGACAAC
CTAATGCAAGAAGCCAGCCATCCAAAACTCTGTTTGTCAAAGGTCTATCTGAGGATACTACAGAAGAGACAGTAAAGGAG
TTGTTTGACGGCTCTATTCGTGCAAGGATAGTCACTGACCGGGAGGCTGGATCCTCTAAGGGGTTTGGTTTTGTAGACTT
CAACAGCGAGGAAGAGGCCAAAGCTGTCAAGGAGGCCATGGAAGATGGCGAAATCGATGGAAACAAAGTTACTTTGGACT
GGGCCAAGCCTAAGGGT

Alignment

ORF - retro_ttru_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.99 %
• Parental protein coverage: 53.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELVKEAPGKRKKEMAKQKAAPEAKKQKVEATEPTTSFNLFVGNLNFSKSAPELKTGISDLFAKNDLAVVD
          ELVKEAPGKR.KEMAKQKAAPEAKKQKVEATEPTTSFNLFVGNLNFSKSAPE.KTG.SDLFAKNDLAVVD
Retrocopy ELVKEAPGKRTKEMAKQKAAPEAKKQKVEATEPTTSFNLFVGNLNFSKSAPEMKTGFSDLFAKNDLAVVD

Parental  VRIGVSRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQEELK
          VRIGVSRKFGYVDFE.AEDLE.ALELTGLKVFGNEIKLEKPKGKDSKKE.DARTLLAKNLPYKVTQEELK
Retrocopy VRIGVSRKFGYVDFEPAEDLEQALELTGLKVFGNEIKLEKPKGKDSKKEQDARTLLAKNLPYKVTQEELK

Parental  EVFEDAVEIRLVSKDGKSKGIAYIEFKTEADAEKTLEEKQGTEIDGRSISLYYTGEKGQGQDHRGGKNST
          EVFED.VEIRLVSKDGK.KGIAYIE..TEADAEKTLEEKQGTEIDGRSISLYYTGEKGQ.QD.RGGKNST
Retrocopy EVFEDTVEIRLVSKDGKCKGIAYIESRTEADAEKTLEEKQGTEIDGRSISLYYTGEKGQSQDYRGGKNST

Parental  WTGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQSGKSKGYAFIEFASFEDAKEALNSCNKREIEG
          WTGESKTLVLSNLSYSA.EETLQEVFEKATFIKVPQNQ.GKSKGYAFIEFASFEDAKEALNSCNKREIEG
Retrocopy WTGESKTLVLSNLSYSAMEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEG

Parental  RAIRLELQGPRGQPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSE
          RAIRLELQGPRGQPNARSQPSKTLFVKGLSEDTTEET.KE.FDGS.RARIVTDRE.GSSKGFGFVDFNSE
Retrocopy RAIRLELQGPRGQPNARSQPSKTLFVKGLSEDTTEETVKELFDGSIRARIVTDREAGSSKGFGFVDFNSE

Parental  EEAKAAKEAMEDGEIDGNKVTLDWAKPKG
          EEAKA.KEAMEDGEIDGNKVTLDWAKPKG
Retrocopy EEAKAVKEAMEDGEIDGNKVTLDWAKPKG

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_51 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_51 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 ,