RetrogeneDB ID: retro_ttru_490

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2463:31542..32111(-)
• Located in intron of: ENSTTRG00000007422

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11C
• Ensembl ID: ENSTTRG00000007676
• Aliases: None
• Description: SEC11 homolog C (S. cerevisiae) [Source:HGNC Symbol;Acc:23400]

Sequence

>retro_ttru_490
GTGCGCATGGGCACCGTGGGGTCACATCTCCCCGCGTCCGGCTTGGACACCTTTGGGGACCCGAGGAAGATGAACAAGCA
CCAGCTCTATTACTTGGTCTTAAACTTCGCCATGACTGTGTCTTCTGCGCTCATGGTCTGGAAAGGCCTGATCGTCCTCA
CTGGCAGCGGGAGTCCCATCGTGGTGGTGCTGAGTGACAGCGTGGGCCAGCCTTTCACAGGGGTCACCTTCTGTTCCTAA
CAAATTCCCTGGAACACCCGATTAGAGCTGCTGAAATCGTTGCTTTTAAAGTCGAAAGACGAGACATTCCAATAGTTCAC
AGAGTTATCAAAGTTCATGAAAAAGATAATGGAGACATCACATTTCTGACCAGGGGAGATAATAATGACATTGGGGATAG
AGGCTAGTACAAAGAAGGCCAGAGCTGGCTCGAAAAGAGGGACATGTTGGGGAGAGCCAGAGGGTTTTTACCATAGGTTG
GCATGGTCACCATAATAATGAACGACCATCCAAAATCCAGGTGTGCTCTTTGGGTTGTAATGGGCGCATATGTGCTACTA
AAACGTGAA

Alignment

ORF - retro_ttru_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.63 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRAGAVGSHLPASGLDIFGDLRKMNKRQLYYQVLNFAMIVSSALMIWKGLIVLTGSESPIVVVLSGSME-
          VR.G.VGSHLPASGLD.FGD.RKMNK.QLYY.VLNFAM.VSSALM.WKGLIVLTGS.SPIVVVLS.S...
Retrocopy VRMGTVGSHLPASGLDTFGDPRKMNKHQLYYLVLNFAMTVSSALMVWKGLIVLTGSGSPIVVVLSDSVG<

Parental  PAFHRGDLLFLTNFREDPIRAGEIVVFKVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNEVDDRGLYKE
          PAFHRG.LLFLTN..E.PIRA.EIV.FKVE.RDIPIVHRVIKVHEKDNGDI.FLT.GDNN...DRG.YKE
Retrocopy PAFHRGHLLFLTNSLEHPIRAAEIVAFKVERRDIPIVHRVIKVHEKDNGDITFLTRGDNNDIGDRG*YKE

Parental  GQNWLEKKDVVGRARGFLPYVGMVTIIMNDYPKFKYALLAVMGAYVLLKRE
          GQ.WLEK.D..GRARGFLP.VGMVTIIMND.PK...AL..VMGAYVLLKRE
Retrocopy GQSWLEKRDMLGRARGFLP*VGMVTIIMNDHPKSRCALWVVMGAYVLLKRE

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_490 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_490 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 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017024	3 retrocopies	retro_ecab_1009, retro_ecab_455, retro_ecab_989,
Echinops telfairi	ENSETEG00000005115	2 retrocopies	retro_etel_1081, retro_etel_1139,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815,
Microcebus murinus	ENSMICG00000016052	1 retrocopy	retro_mmur_271,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517, retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738, retro_ocun_895,
Otolemur garnettii	ENSOGAG00000002570	1 retrocopy	retro_ogar_400,
Pteropus vampyrus	ENSPVAG00000002950	2 retrocopies	retro_pvam_620, retro_pvam_869,
Sus scrofa	ENSSSCG00000004912	1 retrocopy	retro_sscr_775,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357,
Tursiops truncatus	ENSTTRG00000005833	1 retrocopy	retro_ttru_1237,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490 ,