RetrogeneDB ID: retro_ttru_1003

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_960:29991..30579(-)
• Located in intron of: None

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_1003
ATCTCATTTATTTTGAATAAGGAACTTACAGACATTCGGAGTACAGATGGACAACCTGCCCCGGTCATTGCTCCCAGGGA
GCATCAGCTTGTCTTGCAGGGGGTCAGAGGGCAGGTCCTCACGGTGCTGACTGAGCGTGCACCGGATCAGCTCTCCCTGG
AAGGAACGGTGGTACATCGGGGAGAATGCAGACCTGCTCTGAGTGAAAACTACATGAGGCTGAAGAGAAAGCAAATAGAG
GAGCCTTCCAAACCTGCCAGAACCGTACAGAAACTGGAGAAGGTAGTCACGACCAATTATAAACCTGTTGCCAATCATCA
GTACAATATTGAATATGAGAAGAAAAAGAAAGAAAATGGAAAGAGAGTGAAGGCTGATAAAGACCAAGTTTTAACCTTGC
TATTTGCTGCCTTTGAGAAACACCAGTATTATAACATAAAGGACTTGGTTGGTATCACTTTGCAACCTGTGGCGTACCTG
AAGGAAATCTTGAATGAAATCGGTGTTCAGAATGTAAAAGGGCCCCACAAAAACACATGGGAGCTAAAAGCAGAGTACCG
GTATTGTCCGGCAGCAGCTAAGAGTGAG

Alignment

ORF - retro_ttru_1003 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.41 %
• Parental protein coverage: 80.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSFTLNEDLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAASEN
          .SF.LN..L..I....G.PA.V.APREH..VLQ.V.GQ.LTV.TE...D.LSLEG.VV.R.ECRPA.SEN
Retrocopy ISFILNKELTDIRSTDGQPAPVIAPREHQLVLQGVRGQVLTVLTERAPDQLSLEGTVVHRGECRPALSEN

Parental  YMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANHQYNIEYERKKKEDGKRARADKQHVLDMLFSAFEK
          YMRLKR.QIEE.SKP.R..Q.L.KVVTTNYKPVANHQYNIEYE.KKKE.GKR..ADK..VL..LF.AFEK
Retrocopy YMRLKRKQIEEPSKPARTVQKLEKVVTTNYKPVANHQYNIEYEKKKKENGKRVKADKDQVLTLLFAAFEK

Parental  HQYYNLKDLVDITKQPVSYLKEILKEIGIQNVKGIHKNTWELKPEYRHYQVEEKSD
          HQYYN.KDLV.IT.QPV.YLKEIL.EIG.QNVKG.HKNTWELK.EYR......KS.
Retrocopy HQYYNIKDLVGITLQPVAYLKEILNEIGVQNVKGPHKNTWELKAEYRYCPAAAKSE

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_1003 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1003 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,