RetrogeneDB ID: retro_ttru_1244

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_108540:19811..20455(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LITAF
• Ensembl ID: ENSTTRG00000010854
• Aliases: None
• Description: lipopolysaccharide-induced TNF factor [Source:HGNC Symbol;Acc:16841]

Sequence

>retro_ttru_1244
TCGGTGCCGACCGCGCCCCCGTCTTATGAAGAGACAGTTTCTGTTAACAGTTATTACCCCACACTTCCAGCACCCATGCC
TGGGCCGGCCACGGGGCTCATGATGGGCCCGGATGGGAAGGGCATGAATCCGCCTGTGTACTACACCCAGCCAGTGCCTG
TCCCCAATGCCAATGCAACTGCTGTGCAGACAGTTCGCGTGCAGCAGCCCATCTCCTTTTTCGACCGCCCGGTCCAGATG
TGTTGTCCTTCCTGCAACAAGATGATCATGACTCAGCTGTCCTATAATGCCGGCGCCCTCACCTGGCTCTCCTGCCGGAA
CCTGTGCCTGTTGGGGTGCATGGCGGGCTGCTGCTTCATCCCTTTCTGTGTGGACGCCCTGCAGGATGTGGACCACTACT
GTCCCAACTGCAAAGCTCTCCTGGGCACCTACAAGCGTTTGTAGGACTCAGTCAGACCTTAAGGGAGCGGTGTGCTGCAG
GAAGGCCTTTCCGACTCTCACCCAGCCCCGCCCCTGGTGAAGGCTCCATTTTGGTGGGCTCACCTCTCCAGGGTGTCTAC
CTTCGTGTCTTCTTTTGGGAGGGAAATATCGCAAAAATAACACACCTCCGAACCCCAGAAATTGCTGCTTGGTGTCGTGC
ACAG

Alignment

ORF - retro_ttru_1244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVPTAPP-YEETVSVNSYYPTPPAPMPGPTTGLMTGPDGKGMNPPGYYTQPVPVPNANAIAVQTVYVQQP
          SVPTAPP.YEETVSVNSYYPT.PAPMPGP.TGLM.GPDGKGMNPP.YYTQPVPVPNANA.AVQTV.VQQP
Retrocopy SVPTAPPSYEETVSVNSYYPTLPAPMPGPATGLMMGPDGKGMNPPVYYTQPVPVPNANATAVQTVRVQQP

Parental  ISFFDRPVQMCCPSCNKMIVTQLSYNAGALTWLSCGSLCLL-GVCRGLLLHPFLCGRPAGCGPLLSQLQS
          ISFFDRPVQMCCPSCNKMI.TQLSYNAGALTWLSC..LCLL.GV..GLLLHPFLCGRPAGCGPLLSQLQS
Retrocopy ISFFDRPVQMCCPSCNKMIMTQLSYNAGALTWLSCRNLCLL<GVHGGLLLHPFLCGRPAGCGPLLSQLQS

Parental  SPGHLQAFVGLSQT-REPCAAGRPFRLSPSPTPGEGSILVVSSLQGLHLRVFSWGENIAKITHLQTPEIA
          SPGHLQAFVGLSQT.RE.CAAGRPFRLSPSP.PGEGSILV.S.LQG..LRVF.W..NIAKITHL.TPEIA
Retrocopy SPGHLQAFVGLSQTLRERCAAGRPFRLSPSPAPGEGSILVGSPLQGVYLRVFFWEGNIAKITHLRTPEIA

Parental  ASCRAQ
          A.CRAQ
Retrocopy AWCRAQ

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_1244 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1244 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006659	1 retrocopy	retro_cpor_704,
Macaca mulatta	ENSMMUG00000008784	1 retrocopy	retro_mmul_1411,
Monodelphis domestica	ENSMODG00000005014	4 retrocopies	retro_mdom_174, retro_mdom_574, retro_mdom_887, retro_mdom_911,
Otolemur garnettii	ENSOGAG00000028239	2 retrocopies	retro_ogar_1479, retro_ogar_2820,
Pteropus vampyrus	ENSPVAG00000009213	1 retrocopy	retro_pvam_261,
Rattus norvegicus	ENSRNOG00000002520	1 retrocopy	retro_rnor_2056,
Tupaia belangeri	ENSTBEG00000017097	1 retrocopy	retro_tbel_4388,
Tursiops truncatus	ENSTTRG00000010854	1 retrocopy	retro_ttru_1244 ,