RetrogeneDB ID: retro_tsyr_863

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_22235:10634..11953(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMEK1
• Ensembl ID: ENSTSYG00000010333
• Aliases: None
• Description: SMEK homolog 1, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:20219]

Sequence

>retro_tsyr_863
TCACTGCTCTTGTTGTCTAAAATAGATCCAGAAACGGTTTATAAGAAACCACAAGCGGAGTTAATTATGTGGTCTGAAGC
CGAATACCATGGCATCGCAAGAATTTCCAGGAAAGAGCGGGTTGTCAGGACATCTGGGAGGACATTTGCCGCATTCAAGG
TAAAGACCCACTTGCCGCAATCACACAGGACCTATTGCATGAATCAGAAGAAGATCAATTTGATGAGATGCCAGAAATCA
GTAATCTGGTTGAGCTGCCTAACTGTGAACTCAGTACAATAAAACAAATTGATGATTTAGTCACTTCAGTTCTCGAGTCA
CCTATCCGGAGGGAAAGGCTGGCTCTGATATTGGAAAATGAGGATTATATTAAAAAACTACTGCAGCTGTTCCACACTTG
TGAAAACCTAGAGAACATTGAAGGTTTATGCCATTTGCATGACATTATTAAAGGAATCTTATTTCTCAACAAGACATCTC
TGTTTGAGATGATGTTCTCTGATGAGTGTATCATGGATGTGGTGGGATGCCTTGAATACGACCCTGCTTTGGCTCAGCCA
AAAAAGCATAGGGAATTCTTGACCCAAAATGCAAAGTTCAAGGAGGTTATACCAATAACAGACTCTGAACTTAGGCAAAA
AATACATCAGACATACAAAGTACAGTACATTTATGATATACTTTTGCCTACACCATCTATATTTGAAGAGAATATTCTTT
CCACACTTACAATGTTTATTTTCTTCAATAAGGTTGAGATTGTTACCATGCTACAGAAAGATGACAAAATTATGTCTGAA
CTTTTTGCACAGTTACAGAATAAGACTACAGATGATGATAAACGACATGAATTGCTGGTTTTTTTCAAGGAATTCTGTGC
ATTTTCTCAGACCTTACAGCCTCAAAACAAGGATGCACTATTAAAAACATTGACAAAATTGGGAATTCTTCCTACTCTTA
AAATTGTAATGAGCATAGGTGATTTGCAAATAAGGTCAGCTGCTACAGATATATTTGCTTATCTAGTGGAGTACAGTCCA
TCCACGATCCGCGAATTTGTAATGAAAGAGGAGAGCAAAGATGGTGACCTTTTCATTAATATAGTAATTGAACAAATGAT
TTGTGATACTGATCCTGAGCTAGGAGGTGCTGTTCATTTGATGGGACTTCTTCGCGCTCTGCTTGATCCAAGCAATATGC
TGGTAACACCTAATAAATGTGAAAGAAGTGGATTTCTAAATTTCTTCTATAAACGTTGTATGAATAACTTTATAGCACCA
CTTTTGGCCACCACTTCAGAAGACAAATGTGCAAAGGAT

Alignment

ORF - retro_tsyr_863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.82 %
• Parental protein coverage: 56.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLLLESKINPNTAYQKQQDTLIVWSEAENYDLAL-SFQEKAGCDEIWEKICQVQGKDPSVDITQDLVDES
          SLLL.SKI.P.T.Y.K.Q..LI.WSEAE....A...FQE.AGC..IWE.IC..QGKDP...ITQDL..ES
Retrocopy SLLLLSKIDPETVYKKPQAELIMWSEAEYHGIAR<NFQERAGCQDIWEDICRIQGKDPLAAITQDLLHES

Parental  EEERFDDMS--SPGLELPSCELSRLEEIAELVASSLPSPLRREKLALALENEGYIKKLLELFHVCEDLEN
          EE..FD.M...S...ELP.CELS....I..LV.S.L.SP.RRE.LAL.LENE.YIKKLL.LFH.CE.LEN
Retrocopy EEDQFDEMPEISNLVELPNCELSTIKQIDDLVTSVLESPIRRERLALILENEDYIKKLLQLFHTCENLEN

Parental  IEGLHHLYEIIKGIFLLNRTALFEVMFSEECIMDVIGCLEYDPALSQPRKHREFLTKTAKFKEVIPISDP
          IEGL.HL..IIKGI..LN.T.LFE.MFS.ECIMDV.GCLEYDPAL.QP.KHREFLT..AKFKEVIPI.D.
Retrocopy IEGLCHLHDIIKGILFLNKTSLFEMMFSDECIMDVVGCLEYDPALAQPKKHREFLTQNAKFKEVIPITDS

Parental  ELKQKIHQTYRVQYIQDMVLPTPSVFEENMLSTLHSFIFFNKVEIVGMLQEDEKFLTDLFAQLTDEATDE
          EL.QKIHQTY.VQYI.D..LPTPS.FEEN.LSTL..FIFFNKVEIV.MLQ.D.K....LFAQL....TD.
Retrocopy ELRQKIHQTYKVQYIYDILLPTPSIFEENILSTLTMFIFFNKVEIVTMLQKDDKIMSELFAQLQNKTTDD

Parental  EKRQELVNFLKEFCAFSQTLQPQNRDAFFKTLSNMGILPALEVILGMDDTQVRSAATDIFSYLVEYNPSM
          .KR.EL..F.KEFCAFSQTLQPQN.DA..KTL...GILP.L.......D.Q.RSAATDIF.YLVEY.PS.
Retrocopy DKRHELLVFFKEFCAFSQTLQPQNKDALLKTLTKLGILPTLKIVMSIGDLQIRSAATDIFAYLVEYSPST

Parental  VREFVMQEAQQNDDDILLINLIIEHMICDTDPELGGAVQLMGLLRTLVDPENMLATANKTEKTEFLGFFY
          .REFVM.E.....D..L.IN..IE.MICDTDPELGGAV.LMGLLR.L.DP.NML.T.NK.E...FL.FFY
Retrocopy IREFVMKEESKDGD--LFINIVIEQMICDTDPELGGAVHLMGLLRALLDPSNMLVTPNKCERSGFLNFFY

Parental  KHCMHVLTAPLLANTTEDKPSKD
          K.CM....APLLA.T.EDK..KD
Retrocopy KRCMNNFIAPLLATTSEDKCAKD

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_863 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000012467	1 retrocopy	retro_dord_714,
Erinaceus europaeus	ENSEEUG00000006324	1 retrocopy	retro_eeur_316,
Pan troglodytes	ENSPTRG00000006638	1 retrocopy	retro_ptro_124,
Pteropus vampyrus	ENSPVAG00000015294	1 retrocopy	retro_pvam_1091,
Tupaia belangeri	ENSTBEG00000008535	1 retrocopy	retro_tbel_2368,
Tarsius syrichta	ENSTSYG00000010333	1 retrocopy	retro_tsyr_863 ,
Tursiops truncatus	ENSTTRG00000013598	1 retrocopy	retro_ttru_1398,
Vicugna pacos	ENSVPAG00000002765	1 retrocopy	retro_vpac_536,