RetrogeneDB ID: retro_ttru_697

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3108:274410..274885(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB28
• Ensembl ID: ENSTTRG00000003622
• Aliases: None
• Description: RAB28, member RAS oncogene family [Source:HGNC Symbol;Acc:9768]

Sequence

>retro_ttru_697
ATGTCGGACTCTTGAGGAGGAGAGCCAGGACCAGCAACTGAGAATCGTCGTGCTGGGGGGCGGCACCTCAGGGCAGACCT
CCTTAGCTACGTGTTTTGCTCAAGGAGCTTTTGGGAAACAGTACAAACTATAGGACTGGATTTCTTTTTGAGAAGAATAA
CGTTGCCAGGAAACTTGAATGTTACTCTTCAAGTCTGGGACATAGGAGAGCAGACAATGGGAGGCAAGCTGTTGGATAAA
TGTATGTATGGAGCACAGGGAATCCCTCTTGGTATATGATATTACAAATTATCAAAGCTTTGAGAATTTAGAAGATTGGT
ATTCTGTGGTGAGGAATGTGAGGGAGGAATCAGAAACTCGGCCACTGGCTGCCTTGGTGGGCAATAAAATTGATTTGGAG
CATATGCAAATGATAAAACCTGAAAAACACTTAAGGTTTTGCCAGGAAAATGGTTTTAGTAGCCACTGTCTCAGC

Alignment

ORF - retro_ttru_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 71.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSDS-EEESQDRQLKIVVLGDGTSGKTSLATC-FAQETFGKQYKQTIGLDFFLRRIMLPGNLNVTLQVWD
          MSDS.EEESQD.QL.IVVLG.GTSG.TSLATC.F....F.....QTIGLDFFLRRI.LPGNLNVTLQVWD
Retrocopy MSDS>EEESQDQQLRIVVLGGGTSGQTSLATC<FCSRSFWETV-QTIGLDFFLRRITLPGNLNVTLQVWD

Parental  IGGQTIGGKMLDKYIYGAQGI-LLVYDITNYQSFENLEDWYSVVKKVSEESETQPLVALVGNKIDLEHMR
          IG.QT.GGK.LDK..YGAQGI.LLVYDITNYQSFENLEDWYSVV..V.EESET.PL.ALVGNKIDLEHM.
Retrocopy IGEQTMGGKLLDKCMYGAQGI>LLVYDITNYQSFENLEDWYSVVRNVREESETRPLAALVGNKIDLEHMQ

Parental  TVKPEKHLRFCQENGFSSHFVS
          ..KPEKHLRFCQENGFSSH..S
Retrocopy MIKPEKHLRFCQENGFSSHCLS

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_697 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_697 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
Ailuropoda melanoleuca	ENSAMEG00000009344	1 retrocopy	retro_amel_469,
Dipodomys ordii	ENSDORG00000012378	1 retrocopy	retro_dord_682,
Macropus eugenii	ENSMEUG00000006792	4 retrocopies	retro_meug_1079, retro_meug_1182, retro_meug_1510, retro_meug_913,
Macaca mulatta	ENSMMUG00000022025	1 retrocopy	retro_mmul_1172,
Sarcophilus harrisii	ENSSHAG00000009274	1 retrocopy	retro_shar_602,
Sus scrofa	ENSSSCG00000022358	2 retrocopies	retro_sscr_482, retro_sscr_514,
Ictidomys tridecemlineatus	ENSSTOG00000004135	1 retrocopy	retro_itri_27,
Tursiops truncatus	ENSTTRG00000003622	1 retrocopy	retro_ttru_697 ,