RetrogeneDB ID: retro_ttru_554

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2668:205808..207357(-)
• Located in intron of: ENSTTRG00000008368

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP1
• Ensembl ID: ENSTTRG00000013871
• Aliases: None
• Description: ubiquitin specific peptidase 1 [Source:HGNC Symbol;Acc:12607]

Sequence

>retro_ttru_554
AGACTTTCCTTGAAGTTTTTTCAGAAAAAGGAAACCAAGAGAGCCTTGGATTTCACAGATTCTCAAGAAAATGAAGAAAA
AACTTCTGAATATAGAGGGTCTGAAACTGATCAAGCTGTTCCTGCAGCACAGTCCTCACGTATCAACTGTGAGAAGAGAG
AAAACTTGTTACCGTTTGTGGGACTGAATAATCTCGGCAATACTTGTTATCTTAATAGTGTACTTCAGGTAGTATGTTTT
TGTCCTGGTTTTAGATCTGGAGTGAAGCACTTATTTAATATTATTTCAAGGAAGAAAGAAGCCCTAAAAGATGAAGCCAG
TCAAAAAGATAAGGGAAGTTGCAAAGATGATTCTTCAGCAAGTTATGAACTAATATGCAGCTTACAGTCCTTGATCATTT
CAGTCGAACAGCTTCAGGCTAGTTTTCTCTTAAATCCAGAGAAATATACTGGTGAACTGGCTACTCAGCCAGGGCGACTA
CTTAACACACTCAGGGAACTCAAGCCTGTGTGTGAAGGATATCTACAGCGTGATGCACAGGAAGTATTACAGTGGATTTT
GGGAAACATTCAAGAAACATGCCAACTCCTAAAGAAAGACGTAAAAAATGTGGCAGAGTTATCTACTAAGGTAGAAGAAA
CACATCAGAAAGAGGAAATGAGTGGTAATAACAGCATGGAGATGGACAGTATGAGGCATTCGGAAGACTATAAAGAAAAA
TTGCCAGAAGTAAATGGGAAAAGAAAAAAGTGACACTGAATTTGGTAACATGAAGGAAAAAGTTAAAGTCTCTAAGGAAC
ACCAGTCTTTGGAAGAAAACCAGAGACAAACCAGATCAAAAAGAAAAGCTACAGTTGATTCATTAGATATTCCTGCTAAA
ATAATCCCCAAGTGCATTTCTGAAAATGAGAGTGCAGGACCCTCACAAAAGAAATCAAGAGTTAAAATAAACTGGTTAAA
GTCTGCAGCTAAGCAGCCCAGCATTATTTCTAAATTCTGTAGTCTGGGTAAAATAACAACAAACCAAGAATCCAAAGGAC
AATCTAAAGAAAATGAATATGATCTTGAAGAGGACTTGGGGAAGTATGAGAATGATAATACAGCTAATGGTTGTGTACTT
GAATCTCCAGGGAATAATGTTATGCCTGTTAATGAAGTTAAGCCCATAAACAAAGGTGCAGAGCAAATTGGTTTTGAGCT
AGTGGAGAAATTATTTCAAGGCCAGCTGGTATTAAGGACTCATTGCTTAGAATGTGAAAGTTTAACAGAAAGAAGAGAAG
ATTTTCAAGACATCAGTGTACCAGTGCAAGAAGATGAGCTTTCCAAAGTAGAGGAGAGTTCTGAAATTTCTCTAGAGCCA
AAAACAGAAATGAAGACCCTGAGATGGGCAATTTCAGAGTTTGCCTCAGTGGAGAGGATTGTAGGAGAAGATAAATATTT
CTGTGAAAATTGCCATCATTATACTGAAGCTGAACGAAGTCTTTTGTTTGACAAAATGCCTGAAGTTATAACTATTCATT
TGAAGTGCTTTGCTGCTAGTGGCTTGGAG

Alignment

ORF - retro_ttru_554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94. %
• Parental protein coverage: 66.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLSLKFFQKKETKRALDFTDSQENEEKTSEYRGSEIDQVVPAAQSSPVNCEKRENLLPFVGLNNLGNTCY
          RLSLKFFQKKETKRALDFTDSQENEEKTSEYRGSE.DQ.VPAAQSS..NCEKRENLLPFVGLNNLGNTCY
Retrocopy RLSLKFFQKKETKRALDFTDSQENEEKTSEYRGSETDQAVPAAQSSRINCEKRENLLPFVGLNNLGNTCY

Parental  LNSILQVLYFCPGFKSGVKHLFNIISRKKEALKDEASPKDKGSCKEDSSASYELICSLQSLIISVEQLQA
          LNS.LQV..FCPGF.SGVKHLFNIISRKKEALKDEAS.KDKGSCK.DSSASYELICSLQSLIISVEQLQA
Retrocopy LNSVLQVVCFCPGFRSGVKHLFNIISRKKEALKDEASQKDKGSCKDDSSASYELICSLQSLIISVEQLQA

Parental  SFLLNPEKYTDELATQPRRLLNTLRELNPMYEGYLQHDAQEVLQCILGNIQETCQLLKKEVKNVAELSTK
          SFLLNPEKYT.ELATQP.RLLNTLREL.P..EGYLQ.DAQEVLQ.ILGNIQETCQLLKK.VKNVAELSTK
Retrocopy SFLLNPEKYTGELATQPGRLLNTLRELKPVCEGYLQRDAQEVLQWILGNIQETCQLLKKDVKNVAELSTK

Parental  VEEKHQKEEMSGNNSMEMDSMRHCEDYKEKLPKVNGKRK-SDTEFGNMKKKVKVSKEHQSLEENQRQTRS
          VEE.HQKEEMSGNNSMEMDSMRH.EDYKEKLP.VNGKRK.SDTEFGNMK.KVKVSKEHQSLEENQRQTRS
Retrocopy VEETHQKEEMSGNNSMEMDSMRHSEDYKEKLPEVNGKRK>SDTEFGNMKEKVKVSKEHQSLEENQRQTRS

Parental  KRKATVDSLDIPAKIIPKYISENESARPSQKKSRVKINWLKSAAKQPSIISKFCSLGKITTNQESKGQCK
          KRKATVDSLDIPAKIIPK.ISENESA.PSQKKSRVKINWLKSAAKQPSIISKFCSLGKITTNQESKGQ.K
Retrocopy KRKATVDSLDIPAKIIPKCISENESAGPSQKKSRVKINWLKSAAKQPSIISKFCSLGKITTNQESKGQSK

Parental  ENEYDLEEDLGKYENDNTANGCGLESPGNNVMPANEVKPINKGAEQIGFELVEKLFQGQLVLRTRCLECE
          ENEYDLEEDLGKYENDNTANGC.LESPGNNVMP.NEVKPINKGAEQIGFELVEKLFQGQLVLRT.CLECE
Retrocopy ENEYDLEEDLGKYENDNTANGCVLESPGNNVMPVNEVKPINKGAEQIGFELVEKLFQGQLVLRTHCLECE

Parental  SLTERREDFQDISVPVQEDELSKVEESSEISPEPKTEMKTLRWAISQFASVERIVGEDKYFCENCHHYTE
          SLTERREDFQDISVPVQEDELSKVEESSEIS.EPKTEMKTLRWAIS.FASVERIVGEDKYFCENCHHYTE
Retrocopy SLTERREDFQDISVPVQEDELSKVEESSEISLEPKTEMKTLRWAISEFASVERIVGEDKYFCENCHHYTE

Parental  AERSLLFDKMPEVITIHLKCFAASGLE
          AERSLLFDKMPEVITIHLKCFAASGLE
Retrocopy AERSLLFDKMPEVITIHLKCFAASGLE

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_554 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_554 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012439	1 retrocopy	retro_mluc_1727,
Mus musculus	ENSMUSG00000028560	1 retrocopy	retro_mmus_2136,
Otolemur garnettii	ENSOGAG00000009357	1 retrocopy	retro_ogar_3339,
Tursiops truncatus	ENSTTRG00000013871	1 retrocopy	retro_ttru_554 ,