RetrogeneDB ID: retro_tsyr_1126

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_31588:16134..17049(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2H3
• Ensembl ID: ENSTSYG00000007444
• Aliases: None
• Description: general transcription factor IIH, polypeptide 3, 34kDa [Source:HGNC Symbol;Acc:4657]

Sequence

>retro_tsyr_1126
ATGGTGTCAGACGAAAATGAATTAAATCTTCTAATTATCATAGTTGATACCAACCCAATTTGGTGGGGAAAGCAAGCATT
GAAGGAGTCTCAGTTTACTTTATCCAAATTCATACATGTCATGATGGTTCTGGGAAATTTCCATTTGTTCATAAATCATT
ACAAAAAACTTGCTGTGACAGCAAGTCACATTCAAGAAAGTCAATTTTTATATCCTGGGAAGAATGGCTAATTTGGGGAC
CCTGGAAACCCTCCTTCTGAATTTAATCCCTCTGAGAATAAATATGGAAAATACAAGCTATTAAAAGCAGCAAATGAAGT
TATTACTGAAGAGATTAAGGAACTAATGGCCAAGAGTGACATAAAGGGCCAGCATACAGAGGCTCTGCTTACTGGATCCC
TGGCCAAAGTCCTTTGCTACATTAATAGAATGAACAAGGAAGTTCAAAATAATCAGGAGATAGGATCAAGAATATTGGTG
ATTAAGGCTACAGAAGATAGTGCATTGCAGTATATGAACTTCATGAATGTCATCTTCGCAGCACAGAAATAGAATATTTT
GATTGATGCCTGTGGTTTAGACTCCAACTCAGGCCTCCTACAACTGGCTTGTGACATCACAGGAGGGCTGCACTTGAAGG
TGCCTCAGATGTCCTCCCTTCTGCAGTATTTGCTGTAGGTATTTCTCCCTGATCAAGATCAGAGATCTCAGTCAATCCTC
CCACTCCCAATTCATGTCGACTTCAGGGCCTCTTACTTCTGTCATCAAAGTCTCATTGAAATTCCCTATGTCTGTTTTGT
GTGTTTGTCAATATTCTGCAATTTCAGCCCAATCTGCACTACATGTGAAACAGCCTTTAAGATTTCTCTGCCTCCTGTAC
TAAAGGTCAAGAAAAAGAAACTGAAAGTGCCTGCA

Alignment

ORF - retro_tsyr_1126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSDEDELNLLVIIVDTNPIWWGKQALKESQFTLSKCIDAVMVLGNSHLFMNRSNKLAVIASHIQESRFL
          MVSDE.ELNLL.IIVDTNPIWWGKQALKESQFTLSK.I...MVLGN.HLF.N...KLAV.ASHIQES.FL
Retrocopy MVSDENELNLLIIIVDTNPIWWGKQALKESQFTLSKFIHVMMVLGNFHLFINHYKKLAVTASHIQESQFL

Parental  YPGKNGRVGDFFGDPGNPPSEFNPSGSKDGKYELLTAANEVIAEEIKDLMTKSDIKGQQTEALLAGSLAK
          YPGKNG..GD....PGNPPSEFNPS..K.GKY.LL.AANEVI.EEIK.LM.KSDIKGQ.TEALL.GSLAK
Retrocopy YPGKNG*FGD----PGNPPSEFNPSENKYGKYKLLKAANEVITEEIKELMAKSDIKGQHTEALLTGSLAK

Parental  ALCYIHRMNKEVKDNQEMKSRILXXXXXXXXXXXXXXXXXXXFAAQKQNILIDACVLDSDSGLLQQACDI
          .LCYI.RMNKEV..NQE..SRIL...................FAAQK.NILIDAC.LDS.SGLLQ.ACDI
Retrocopy VLCYINRMNKEVQNNQEIGSRILVIKATEDSALQYMNFMNVIFAAQK*NILIDACGLDSNSGLLQLACDI

Parental  TGGLYLKVPQMPSLLQYLLWVFLPDQDQRSQLILPPPIHVDYRAACFCHRNLIEIGYVCSVCLSIFCNFS
          TGGL.LKVPQM.SLLQYLL.VFLPDQDQRSQ.ILP.PIHVD.RA..FCH..LIEI.YVC.VCLSIFCNFS
Retrocopy TGGLHLKVPQMSSLLQYLL*VFLPDQDQRSQSILPLPIHVDFRASYFCHQSLIEIPYVCFVCLSIFCNFS

Parental  PICTTCETAFKISLPPVLKAKKKKLKVSA
          PICTTCETAFKISLPPVLK.KKKKLKV.A
Retrocopy PICTTCETAFKISLPPVLKVKKKKLKVPA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1126 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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,