RetrogeneDB ID: retro_ttru_850

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3640:294389..294773(-)
• Located in intron of: ENSTTRG00000001240

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2F2
• Ensembl ID: ENSTTRG00000002729
• Aliases: None
• Description: general transcription factor IIF, polypeptide 2, 30kDa [Source:HGNC Symbol;Acc:4653]

Sequence

>retro_ttru_850
AGGATGGAGGTGTCATTTACTTTGAATGAGGCCCTTGCAAATATTCATGATATTGGCGGAAAATCAGCTTCAGGCAGTGC
TCCTAGAGTACATATATTTGTCTTGCAAAGTGTTGGGGGACAGGCATTAACAGTGTCTAATAAGAGCTCATCGGATAAGC
TTTCACTGGAAGGAATAGTGGTACAAAGAGTTGAATGTTGACCCACTGCCAGTGAAAAGTACATGAGATTAAAGAGATTA
CAAATAGAAGAATCTTCCAAACCTGTAAGGCTATTACAGCAACTGAACAAAGCTGTGACAACCAATTACAAACCTGTTGT
TAATCATCAGTACAATATTGAATATGAAAGGAAAAAGAAAGATGGAAAACGAGCTCGAGCTGAT

Alignment

ORF - retro_ttru_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.5 %
• Parental protein coverage: 53.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RIAVSFTLNEDLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAA
          R..VSFTLNE.LANIHDIGGK.AS.SAPR.H.FVLQSVGGQ.LTV...SSSDKLSLEGIVVQR.EC.P.A
Retrocopy RMEVSFTLNEALANIHDIGGKSASGSAPRVHIFVLQSVGGQALTVSNKSSSDKLSLEGIVVQRVEC*PTA

Parental  SENYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANHQYNIEYERKKKEDGKRARAD
          SE.YMRLKRLQIEESSKPVRL.QQL.K.VTTNYKPV.NHQYNIEYERKKK.DGKRARAD
Retrocopy SEKYMRLKRLQIEESSKPVRLLQQLNKAVTTNYKPVVNHQYNIEYERKKK-DGKRARAD

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_850 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_850 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028333	1 retrocopy	retro_acar_174,
Bos taurus	ENSBTAG00000034495	2 retrocopies	retro_btau_1753, retro_btau_208,
Choloepus hoffmanni	ENSCHOG00000007391	1 retrocopy	retro_chof_1718,
Felis catus	ENSFCAG00000002105	1 retrocopy	retro_fcat_526,
Myotis lucifugus	ENSMLUG00000010505	1 retrocopy	retro_mluc_58,
Monodelphis domestica	ENSMODG00000025484	1 retrocopy	retro_mdom_231,
Nomascus leucogenys	ENSNLEG00000002097	1 retrocopy	retro_nleu_2440,
Nomascus leucogenys	ENSNLEG00000002106	1 retrocopy	retro_nleu_742,
Procavia capensis	ENSPCAG00000005868	3 retrocopies	retro_pcap_102, retro_pcap_173, retro_pcap_375,
Pongo abelii	ENSPPYG00000005333	1 retrocopy	retro_pabe_93,
Pteropus vampyrus	ENSPVAG00000014092	1 retrocopy	retro_pvam_1490,
Rattus norvegicus	ENSRNOG00000029316	1 retrocopy	retro_rnor_1288,
Ictidomys tridecemlineatus	ENSSTOG00000006891	1 retrocopy	retro_itri_19,
Tursiops truncatus	ENSTTRG00000002729	2 retrocopies	retro_ttru_1003, retro_ttru_850 ,