RetrogeneDB ID: retro_ttru_859

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_382:297083..297566(+)
• Located in intron of: ENSTTRG00000004379

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2E2
• Ensembl ID: ENSTTRG00000012464
• Aliases: None
• Description: general transcription factor IIE, polypeptide 2, beta 34kDa [Source:HGNC Symbol;Acc:4651]

Sequence

>retro_ttru_859
GAAGTAATAGATGGAAAGTATGCCTTCAAGCCCAAGTACAACTTGAAAGATAAGAAGGTCCTACTTAGGCTCTTAAATAA
GCATGATCAGCAAGGCTTAGGAGGAATTCTTTTAGAAGACATTGGGGAAGGACTGCCCAATTCCCAGAAAGCAGTTAAGG
ATTCAGGGAACCAGATACCATTTGTAAACCTTCCTGATAAGAAGAAAATTCTTTTCTTCAATGATAAGAGCTGTCAGTTT
TCTGTGGATGAGAAGTTTCAGAAACTGTGAAGGAGTGTCACCGTGGATTCAAGGGATGAGGAGAAAACTGAAGAATATCT
AAAGTGACAGGGTATTTCTTCCATGCAGGAATCTGGACCAAAGAAAGTGGCCCCTATTCAGAGAAAGAAAAAGCCTGCTT
CACAGAAAAAGCGATGGTTTAAGCCTCACAATGAGCACTTGGCCTGGGTGCTGAAGGACTACTCTGACATCGCTCCTGGC
AAG

Alignment

ORF - retro_ttru_859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 70.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVIDGKYAFKPKYNLKDK-ALLRLLDKHDQRGLG-ILLEDIEEGLPNSQKAVKALGDQILFVNRPDKKKI
          EVIDGKYAFKPKYNLKDK..LLRLL.KHDQ.GLG.ILLEDI.EGLPNSQKAVK..G.QI.FVN.PDKKKI
Retrocopy EVIDGKYAFKPKYNLKDKKVLLRLLNKHDQQGLGGILLEDIGEGLPNSQKAVKDSGNQIPFVNLPDKKKI

Parental  LFFNDKSCQFSVDEEFQKLWRSVTVDSMDEEKIEEYLKRQGISSMQESGPKKVAPIQRRKKPASQKKRRF
          LFFNDKSCQFSVDE.FQKL.RSVTVDS.DEEK.EEYLK.QGISSMQESGPKKVAPIQR.KKPASQKKR.F
Retrocopy LFFNDKSCQFSVDEKFQKL*RSVTVDSRDEEKTEEYLK*QGISSMQESGPKKVAPIQRKKKPASQKKRWF

Parental  KTHNEHLAGVLKDYSDITPGK
          K.HNEHLA.VLKDYSDI.PGK
Retrocopy KPHNEHLAWVLKDYSDIAPGK

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_859 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_859 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005031	1 retrocopy	retro_dnov_2321,
Macropus eugenii	ENSMEUG00000010541	1 retrocopy	retro_meug_546,
Myotis lucifugus	ENSMLUG00000007814	1 retrocopy	retro_mluc_2029,
Sorex araneus	ENSSARG00000007758	2 retrocopies	retro_sara_376, retro_sara_569,
Sus scrofa	ENSSSCG00000015845	1 retrocopy	retro_sscr_878,
Tarsius syrichta	ENSTSYG00000013143	1 retrocopy	retro_tsyr_2074,
Tursiops truncatus	ENSTTRG00000012464	1 retrocopy	retro_ttru_859 ,