RetrogeneDB ID: retro_ttru_1684

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_85593:26332..27097(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIM1
• Ensembl ID: ENSTTRG00000001968
• Aliases: None
• Description: pim-1 oncogene [Source:HGNC Symbol;Acc:8986]

Sequence

>retro_ttru_1684
GACCACTTGCCAGTGGCCATCAAGCACGTGGAGAAGGACTGTATTTCAGGCTGGGGAGAGCTGCCTGACGGCACCCGAGT
GCCCATGGAAGTGGTTCTGCTGAAGAAGGTGAGCTCGGGCTTCCCCGGCGTCATCAGGCTCCTGGGCTGGTTCGAGAGAC
CCAGCAGTTTCGCCCTGATCCTGGACAGGCCCGAGCCAGCAGCGCAAGAACGCTTCGACTTAATCACGGAAATGGGGGCC
CTGCAGGCGGAGCTGGCCCACAGCTGCTTCTGGCAGGTGCTGCAGGCCGTGCGGCACTGCCGCAGCTGCGGGGCGCTTCA
CCGCGACGGCAAGGATGAGAACACCCTTATCGACCTCAGTCGCGGTGAGCTCAAACTCATCGACTTCAGGTCGGGGGCGC
TGCTCGAGGACACCGTCTACACGGACTTCGATGGGACCCGAGCATATAGTCCTCCAGAGTGGATCCACTACCATCGCTAC
CATGGCAAGTCAGCAGCCGTCTGGTCTCTGGGGATCCTGCTGTAGGATATGGTCTGTGGAGATATTCCCTTTGAGCACGA
CGAGGAGACCATCAGGGGCCAAGTTTTCTTCAGGCAGAGGGTCTCTTCAGCGTGTCAACATCTCATTAGATGGTGCTTGG
CCCTGAGACCATCAGATCGGCCATCCTTCAAAGAAATCCAGAACCATCCATGGATGCAAGATGTCCTCCTGCCCCAGGAA
ACTGCTGAGATCCATCTCCACAGCCTGTTGCCAAGGCCCAGCAGA

Alignment

ORF - retro_ttru_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.88 %
• Parental protein coverage: 99.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DNCPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPV-QD
          D..PVAIKHVEKD.IS.WGELP.GTRVPMEVVLLKKVSSGF.GVIRLL.WFERP.SF.LIL.RPEP..Q.
Retrocopy DHLPVAIKHVEKDCISGWGELPDGTRVPMEVVLLKKVSSGFPGVIRLLGWFERPSSFALILDRPEPAAQE

Parental  LFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLSRGELKLIDFGSGALLKDTVY
          .FD.ITE.GALQ.ELA.S.FWQVL.AVRHC..CG.LHRD.KDEN.LIDLSRGELKLIDF.SGALL.DTVY
Retrocopy RFDLITEMGALQAELAHSCFWQVLQAVRHCRSCGALHRDGKDENTLIDLSRGELKLIDFRSGALLEDTVY

Parental  TDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIR
          TDFDGTR.YSPPEWI.YHRYHG.SAAVWSLGILL.DMVCGDIPFEHDEE.IRGQVFFRQRVSS.CQHLIR
Retrocopy TDFDGTRAYSPPEWIHYHRYHGKSAAVWSLGILL*DMVCGDIPFEHDEETIRGQVFFRQRVSSACQHLIR

Parental  WCLALRPSDRPSFEEIQNHPWMQDVLLPQETAEIHLHSLLPGPSK
          WCLALRPSDRPSF.EIQNHPWMQDVLLPQETAEIHLHSLLP.PS.
Retrocopy WCLALRPSDRPSFKEIQNHPWMQDVLLPQETAEIHLHSLLPRPSR

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_1684 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1684 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tursiops truncatus	ENSTTRG00000001968	1 retrocopy	retro_ttru_1684 ,