RetrogeneDB ID: retro_ttru_1357

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111333:150920..151845(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2H3
• Ensembl ID: ENSTTRG00000007259
• Aliases: None
• Description: general transcription factor IIH, polypeptide 3, 34kDa [Source:HGNC Symbol;Acc:4657]

Sequence

>retro_ttru_1357
ATGGTCTCAGATGAAGATGAATTGAATCTTCTAGTTATCGTAGTTGATACCAGCCTAATTTGGTGGAGAAAGCAAGCATT
AAAGTAATCTCAGTTTACTTTATCAAAATGCGTAAATGCAGTGATGGTGTTAGGAAATTCTCATTTATTCATGAATCGTT
CCAACAAACTTGCTGTGATAGCAAGTCATATTCAAGAAACTCAATTCTTATATCCCGGAAAGAATGGCAGACTTGGAGAC
TTCTTTGGAGACTCTGGCAACCCTTTTTCTGCACTTAATCCCTCAGGAAGTGAAGATGAAAATATGAGTTGTTAACTTCA
GCAAATGAAATTATTGTTGAAGAGATAAAAGATCTAATGACCAAGAGTGACATAGAGGGTCAACATACAGAAACTCTGCT
GGCAGGATCCCTCGCCAAAGTTGTTTGCTACATTCATGGAATGAACAAGGAGGTTAAAGATAATCAGGAAATGAAATTGT
CTATTGGGTGATTAAGGCTGCAGAAGACAGTGTGTTGCAATATATGAACTTCATGAATGTCAGCTTTGCAGCACAGAAGC
AGAATATTTTGATTGGTGCCTGCGTGTTAGACTCTGATTCAGGACTCCTCCAAAAGGCTTGTGACATCACAGGGGGACTG
TACTTGAAGGTGCCTCAGAGGCCCTCCCTTCTGCAGTATTTACTGTGAGTTTTTCTTCCTGATCAAGATCAGAGATCTCA
GTTAATCCTCCCACCCCCAATTCTTGTTGACTACTGGGCTACTTGATTCTGTCATCGAAATCTCATTGAAATAGGCTACA
TCTGTTCTGTGTGTTTGTCAGTATTCTGCAATTTCAGCCCTATCTGCACTACATGCAAGACAGCCTTTAAGATTTCTCTA
CCTCCAGAACTGAAGGCCAAGAAAAAGTAACTAAAAATGTCTGCA

Alignment

ORF - retro_ttru_1357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVSDEDELNLLVIIVDTNPIWWGKQALKESQFTLSKCIDAVMVLGNSHLFMNRSNKLAVIASHIQESRFL
          MVSDEDELNLLVI.VDT..IWW.KQALK.SQFTLSKC..AVMVLGNSHLFMNRSNKLAVIASHIQE..FL
Retrocopy MVSDEDELNLLVIVVDTSLIWWRKQALK*SQFTLSKCVNAVMVLGNSHLFMNRSNKLAVIASHIQETQFL

Parental  YPGKNGRLGDFFGDPGNASSEFIPSGSKDG-KYELLTAANEVIVEEIKDLMTKSDIEGQHTETLLAGSLA
          YPGKNGRLGDFFGD.GN..S...PSGS.D..KYELLT.ANE.IVEEIKDLMTKSDIEGQHTETLLAGSLA
Retrocopy YPGKNGRLGDFFGDSGNPFSALNPSGSEDE<KYELLTSANEIIVEEIKDLMTKSDIEGQHTETLLAGSLA

Parental  KALCYIHRMSKDVKDNQEMKSRI-LVIKAAEDSTLQYMNFMNVIFAAQK-NILIDACVLDSDSGLLQQAC
          K..CYIH.M.K.VKDNQEMK..I..VIKAAEDS.LQYMNFMNV.FAAQK.NILI.ACVLDSDSGLLQ.AC
Retrocopy KVVCYIHGMNKEVKDNQEMKLSI<WVIKAAEDSVLQYMNFMNVSFAAQKQNILIGACVLDSDSGLLQKAC

Parental  DITGGLYLKVPQMPSLLQYLLWVFLPDQDQRSQLTLPPPVHVDYRAACFCHRNLIEIGYVCSVCLSICLS
          DITGGLYLKVPQ.PSLLQYLL.VFLPDQDQRSQL.LPPP..VDY.A..FCHRNLIEIGY.CSVCLS....
Retrocopy DITGGLYLKVPQRPSLLQYLL*VFLPDQDQRSQLILPPPILVDYWAT*FCHRNLIEIGYICSVCLSVFCN

Parental  ---ICTTCETAFKISLPPVLKAKKKKLKMSA
          ...ICTTC.TAFKISLPP.LKAKKK.LKMSA
Retrocopy FSPICTTCKTAFKISLPPELKAKKK*LKMSA

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_1357 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1357 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006219	2 retrocopies	retro_chof_1726, retro_chof_2064,
Loxodonta africana	ENSLAFG00000007300	1 retrocopy	retro_lafr_292,
Macropus eugenii	ENSMEUG00000013734	1 retrocopy	retro_meug_558,
Myotis lucifugus	ENSMLUG00000004319	1 retrocopy	retro_mluc_183,
Monodelphis domestica	ENSMODG00000023728	1 retrocopy	retro_mdom_1915,
Tupaia belangeri	ENSTBEG00000011048	8 retrocopies	retro_tbel_1645, retro_tbel_1820, retro_tbel_2555, retro_tbel_3550, retro_tbel_3894, retro_tbel_3931, retro_tbel_4065, retro_tbel_4293,
Tarsius syrichta	ENSTSYG00000007444	1 retrocopy	retro_tsyr_1126,
Tursiops truncatus	ENSTTRG00000007259	1 retrocopy	retro_ttru_1357 ,