RetrogeneDB ID: retro_ttru_917

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_64:73737..74337(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC13
• Ensembl ID: ENSTTRG00000004395
• Aliases: None
• Description: SEC13 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:10697]

Sequence

>retro_ttru_917
GGCCTGATCCTGGCCTATGGGAGCTTCAATGGGGCCATCTCCCTACTGACCTATTCCATGTTGGGCCAGTGGGAAGTGAA
GAAGATCAATAACGCTCACACTACTGGCTTCAAAGCAGTGAGCTGGGCCCCTGCTGTCATGCCTGGAAGCTTCATAGACC
AGCCATCTGGGCAGAAGTCCAACTACGTCAAGAAATATGCATCAGGTGGCTGTGACAACCTCATCAAACTGTGGAAGGAG
GAGGAGGACAGCCAGTGGAAGGAAGAGCAGAAGTTGAAAGCACACAGTGACTGGGTTTGAGACATGGCCTGGGCCAGCTC
CATTGGCCTGCCTACCAGCACCATTGCCAGCTGCTCCCAGGATGGTTGAGTGTTCAGTTGTACCTGTGATGATGCCACGG
GCAATACATGGTCTCCCAAACTGTTGCACAAGTTCAATGATGTTGTATGGCATGTGAGCTTGTCCATCACAGCCAACGTC
CTGGCTATCTCAGGCAGAGACAATAACGTGACCCTGTGGAAGGAGTCAGTCAACTGGCAGTGGGTGTGCATCAGTGATGC
CAACAAGGGCCAGGGTTCCATATCCACTTCAGTCACAGAA

Alignment

ORF - retro_ttru_917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84. %
• Parental protein coverage: 54.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLILACGSSDGAISLLTYTGLGQWEVKKINNAHTIGCNAVSWAPAVVPGSLIDQPSGQKPNYIKKFASGG
          GLILA.GS..GAISLLTY..LGQWEVKKINNAHT.G..AVSWAPAV.PGS.IDQPSGQK.NY.KK.ASGG
Retrocopy GLILAYGSFNGAISLLTYSMLGQWEVKKINNAHTTGFKAVSWAPAVMPGSFIDQPSGQKSNYVKKYASGG

Parental  CDNLIKLWKEEEDGQWKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASGNAWSPK
          CDNLIKLWKEEED.QWKEEQKL.AHSDWV.D.AWA.SIGLPTSTIASCSQDG.VF..TCDDA.GN.WSPK
Retrocopy CDNLIKLWKEEEDSQWKEEQKLKAHSDWV*DMAWASSIGLPTSTIASCSQDG*VFSCTCDDATGNTWSPK

Parental  LLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKESVDGQWVCISDVNKGQGSVSTSVTE
          LLHKFNDVVWHVS.SITAN.LA.SG.DN.VTLWKESV..QWVCISD.NKGQGS.STSVTE
Retrocopy LLHKFNDVVWHVSLSITANVLAISGRDNNVTLWKESVNWQWVCISDANKGQGSISTSVTE

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_917 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_917 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917 ,