RetrogeneDB ID: retro_ttru_302

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1817:33654..34093(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HLF
• Ensembl ID: ENSTTRG00000007194
• Aliases: None
• Description: hepatic leukemia factor [Source:HGNC Symbol;Acc:4977]

Sequence

>retro_ttru_302
CATGGCCATAACCTCCACATTCTGGAGTTGTGGCCGGCTGCTCAGTTGGCCCTTCTATCCTGGTCCTGGCATCTGGGTTC
TCTTCACCCATCATCCTGCCTCAAAAGTGCATGAAGAACCCCATCAGTCCAGGTCAGCTGTTGTCAAAAAACCACCAGAC
GTGGAGTCCCATTGATCCTGACACCATTCATGTCCCTGTGGGGTATGAACAAGATCGTTGAGATCTTGGCTTCTCCAGCA
TCCATACCCGGGAAGTGTTTGACTGTAGGAAACCCAGGTTCTCTAAGGTTGTACTGAAACCACAGTCCATGACTAGGGAA
GCTCACAAAGTCTTTATCCTTGGCTGTTGAAATTTACCAAGTCCTGAGCTATGAGTAGAAAGAACAGTACGGCAGCCAAG
TGCTCCTGCCATGCCTGCAGGCTGAAAGAAAATGAGATT

Alignment

ORF - retro_ttru_302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.95 %
• Parental protein coverage: 50.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HDHSPHPPGLQPAS-SAAPSVMDLSSRTSAPIHPGIPSPNCMQSPIRPGQLLPANRNTPSPIDPDTIQVP
          H.H..H...L.PA..S..PS...L.S..S.PI...I....CM..PI.PGQLL..N..T.SPIDPDTI.VP
Retrocopy HGHNLHILELWPAA<SVGPSILVLASGFSSPI---ILPQKCMKNPISPGQLLSKNHQTWSPIDPDTIHVP

Parental  VGYEPDPADLALSSIPGQEMFDPRKRKFSEEELKPQPMIKKARKVFI-PDDLKDDKYWARRRKNNMAAKR
          VGYE.D..DL..SSI...E.FD.RK..FS...LKPQ.M...A.KVFI.P..LK..K..A..RKN..AAK.
Retrocopy VGYEQDR*DLGFSSIHTREVFDCRKPRFSKVVLKPQSMTREAHKVFI<PWLLKFTKS*AMSRKNSTAAKC

Parental  SRDARRLKENQI
          S..A.RLKEN.I
Retrocopy SCHACRLKENEI

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_302 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_302 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016953	1 retrocopy	retro_ecab_224,
Tursiops truncatus	ENSTTRG00000007194	1 retrocopy	retro_ttru_302 ,