RetrogeneDB ID: retro_ttru_1879

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_96868:36125..36940(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPTLC1
• Ensembl ID: ENSTTRG00000008595
• Aliases: None
• Description: serine palmitoyltransferase, long chain base subunit 1 [Source:HGNC Symbol;Acc:11277]

Sequence

>retro_ttru_1879
AGCCATAACATTGTGGTGAATGGAAAAGAAGGTATAAACTTTGCCTCGTTCAATTTTCTTGGATTGTTGGATAACCCCAG
GCTCAAGGCAGCAGCCTTGGCATCTCTAAAGACGTATGGTGTGGGAACTTGTGGACCTAGAGGATTTTATGGCACATTTG
ATGTGCACTTGGATTTGGAAGACCGCCTGGCGAAATTTATGAAGACAGAAGCAGCCATTATACACTCATATGGATTTGCC
GTGATAGCCAGCGCTACTGCAGCTTACTGTAAGAGAGGGGACGTTGTGTCTGTAGATAAAACTGCCTGCTTCGCTATTCA
GAAGGGATTACAGGCATCACGTAGTGAAAGTAAGCTATTTAACCATAATGATACGGATGACCTGGAACAACCACTGAAAG
AACAAGAGACTGAAGATGAAAAGAATCCTTGCAAGGCTCGTGTAACTCGACGTTTCATTGTAGTCGAAGCGTTGTACATG
AATACTGGAACGATTTGCCCTCTTCCAGAACTGGTTCAGTTAAAGTACAAATATAACGCAAGGATCTTTCTGGAGGAAAG
CCTTTTGTTTGGAGTCCTGGGGGAGCATGGCTGAGGAGTCACTGAGCATTCTGGAATCAGTATCGATCATATTGATCTTA
TCAGTGCCAACACGGAGAATTCACTTGCTTCTGTTGGGGGTTTCTGCTGTGGTAGGTCTTCCGTAACTGACCGTTTGTGA
CTTTCCGGCCAGGGACACTGCTTTTCAGGTTCGTTACCCCTCCCCTGTTAGCTGCTGCTGCCACTGAGACCCTCAACATC
ATGGAAGAAAATCCA

Alignment

ORF - retro_ttru_1879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 57.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SHNIVVNGKECINFASFNFLGLLDNPRLKAAALASLKKYGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTE
          SHNIVVNGKE.INFASFNFLGLLDNPRLKAAALASLK.YGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTE
Retrocopy SHNIVVNGKEGINFASFNFLGLLDNPRLKAAALASLKTYGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTE

Parental  EAIIYSYGFATIASAIPAYSKRGDIVFVDKAACFAIQKGLQASRSDIKLFNHNDMDDLDRLLKEQEIEDQ
          .AII.SYGFA.IASA..AY.KRGD.V.VDK.ACFAIQKGLQASRS..KLFNHND.DDL...LKEQE.ED.
Retrocopy AAIIHSYGFAVIASATAAYCKRGDVVSVDKTACFAIQKGLQASRSESKLFNHNDTDDLEQPLKEQETEDE

Parental  KNPRKARVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHFGIDIDD
          KNP.KARVTRRFIVVE.LYMNTGTICPLPELV.LKYKY.ARIFLEESL.FGVLGEHG.GVTEH.GI.ID.
Retrocopy KNPCKARVTRRFIVVEALYMNTGTICPLPELVQLKYKYNARIFLEESLLFGVLGEHG*GVTEHSGISIDH

Parental  IDLISANMENSLASIGGFCCGRSFVIDHQRLSGQGYCFSASLP-PLL-AAAAIEALNIMEENP
          IDLISAN.ENSLAS.GGFCCGRS.V.D...LSGQG.CFS.SLP.P.L.AAAA.E.LNIMEENP
Retrocopy IDLISANTENSLASVGGFCCGRSSVTDRL*LSGQGHCFSGSLP<PPLLAAAATETLNIMEENP

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_1879 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1879 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	ENSTTRG00000008595	1 retrocopy	retro_ttru_1879 ,