RetrogeneDB ID: retro_tsyr_867

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_2230:47282..48898(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCDHGB3
• Ensembl ID: ENSTSYG00000004901
• Aliases: None
• Description: protocadherin gamma subfamily B, 3 [Source:HGNC Symbol;Acc:8710]

Sequence

>retro_tsyr_867
GAGCAGATCCGCTACTCTATACCAGAAGAAATGGCCAGGGGCTCGGTGGTGGGGAACCTCGCCGAGGATCTGGGGCTGCA
TGTCCGGGATTTATTGGCGCGCAACCTCAGAGTTAGTGCAGAGAAGCAATACTTCACCGTGAACACGGAGAATGGAAACA
TACTTGTGAATGACAGAGTGGATCGGGAGTCGCTCTGTCCCCCAAAGCCTCTATGCATCGTGCCTTTAGAGATTGTGGCA
GAAAATCCTCTAAATGTTTTTCACATCAACGTGATGATAGAAGATATCAATGATAACCCACCTCATTTCCCCCACAATAG
CATCATTTTACAAATCAACGAATTTGCAATTCCAGGCACTCGGTTTGGCCTGGAATCTGCTACAGACGCAGACGTAGGGC
CTCACTCTCTCCAGAGTTACCAACTCAGCCCTAGTGAGCATTTCTCTCTGATGATGAAGGGCAAGACTGAAGGCAAGAAT
GCCCCAGAATTGGTGCTGGAGAAGTCCCTGGACCGAGAACAACAGAGCTCCCATCTCCTGGTCCTGACAGCGGTGGACGG
AGGCAAACCTGCCCTAACTGGCACTGTTACAATTCAAATCGAGGTCACTGACGCCAATGATAATGCCCCAGTGTTCAGCC
AGGATCTGTACAAAGTCAGCCTTAGAGAGAACATGCCCCCGGGCACCTCTGTGCTAACGGTGACAGCCACCGACCAGGAT
GAGGGTGTCAATGCAGAGATCACCTACTCTTTCAAATCGCGACGAGATGCTACTGGAAATAGGTTTATGCTAGACCGTCG
AAATGGAGAGATTAAATCCAAAGACTATCTAGACTTTGAAATCAGTAGCAGTTACACCATGAACATAGAAGCGAGAGACG
GTGGAGGCATGACCAGCGAGTGTAAAATTATACTAGAAATTCTAGACGAGAACGACAATGCCCCTGAGGTGACTTTTACT
TCGGTGTCCAGTTCCTTAACTGAGGACGCAGAATCCGGGACTGTGATCGCTCTGTTCAAAACACATGATAAAGATTCGGG
AGAAAACGGAGAGGTCACATGCTTCATAAAAGAAAATGTTCCTTTTAGAATTGAATCTTCCGCCAATAATTACTACAAAC
TAGTAACAGACGGGATCCTGGATCGAGAGCAGACTCCAGAGTACAACGTCACTATCATAGCCACAGACCGGGGCAAGCCG
CCTCTCTCCTCTAGCATAACCGTCACCCTGCACATCGGCGACGTCAACGACAACGCTCCGGTTTTCCAACAGGCATCCTA
CGTGGTCGACGTGGCCGAGAACAACCCACCTGGCGCCTCCATCGCGCAGTCAGCGCCTCGGACCCGGACTTGGGGCCCAA
CGGCCAAGTCTCCTACTCGATCGTGGCCAGCGACCTGGAGCCCGGGTCGCTGTCGTCCTACGTGTCGGTGAGCGCGCAAA
GCGGCGTGTTGTTCGCGCAGCGCGCCTTCAACCACAAGCAGCTGCGCGCCTTCGAGCTGACGCTGCAGGCCCGCGACCAA
GGCTCGCCCGCGCTGGGCGCCCTCGTGACCCTGCGCGTGCTGGTGGGCGACCGCAACGACAACGCGCCGCGGGTGCTGTA
CCCCGCGCTGGGGCCC

Alignment

ORF - retro_tsyr_867 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.7 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQIHYAIPEELAMGALVGNLANDLGFGVRDLPTRNLRVRAE-QKFTVSTENGDLLVNDRID-EQICGKKS
          EQI.Y.IPEE.A.G..VGNLA.DLG..VRDL..RNLRV.AE.Q.FTV.TENG..LVNDR.D.E..C..K.
Retrocopy EQIRYSIPEEMARGSVVGNLAEDLGLHVRDLLARNLRVSAEKQYFTVNTENGNILVNDRVDRESLCPPKP

Parental  MCVLEFEMIAEKPLNFFQVTVLIQDVNDNPPTFSQNITELEISEMALIGATFALESAQDPDVGANSLQQY
          .C....E..AE.PLN.F...V.I.D.NDNPP.F..N...L.I.E.A..G..F.LESA.D.DVG..SLQ.Y
Retrocopy LCIVPLEIVAENPLNVFHINVMIEDINDNPPHFPHNSIILQINEFAIPGTRFGLESATDADVGPHSLQSY

Parental  YLSPNPHFSLIQKENPDGRRYPELVLKAPLDREEQPNHHLVLAAVDGGEPSRSCTTQIRVIVADANDNRP
          .LSP..HFSL..K....G...PELVL...LDRE.Q..H.LVL.AVDGG.P....T..I...V.DANDN.P
Retrocopy QLSPSEHFSLMMKGKTEGKNAPELVLEKSLDREQQSSHLLVLTAVDGGKPALTGTVTIQIEVTDANDNAP

Parental  IFTQDMFRANVQENLPARSSISRVKTTDLDKGVDAEITYAFINIGKAARQLFRLNFNTRELTTSEGLEFE
          .F.QD.......EN.P...S...V..TD.D.GV.AEITY.F.....A....F.L.....E......L.FE
Retrocopy VFSQDLYKVSLRENMPPGTSVLTVTATDQDEGVNAEITYSFKSRRDATGNRFMLDRRNGEIKSKDYLDFE

Parental  ERDRYAVGVETKDGEHHTAYCKRQIDVLDENDNAPEITLASESQHLQEDAELETAIALIKTHDLDSGLNG
          ....Y....E..DG...T..CK.....LDENDNAPE.T..S.S..L.EDAE..T.IAL.KTHD.DSG.NG
Retrocopy ISSSYTMNIEARDGGGMTSECKIILEILDENDNAPEVTFTSVSSSLTEDAESGTVIALFKTHDKDSGENG

Parental  EILC-LKGIFSFKIVRST---HRLVTDGTLDREQIPEYNVTITAT-YSNPPLSSSTSITLHIIDDNDSGP
          E..C..K....F.I..S......LVTDG.LDREQ.PEYNVTI.AT....PPLSSS...TLHI.D.ND..P
Retrocopy EVTCFIKENVPFRIESSANNYYKLVTDGILDREQTPEYNVTIIATDRGKPPLSSSITVTLHIGDVNDNAP

Parental  ISPQASYVIHVPENNQPGASIAQ-VSASDSDLGPNGQGSYWIAAGDGEPRALSSYVSVSAQSGVVLAQRA
          ...QASYV..V.ENN.PGASIAQ.VSASD.DLGPNGQ.SY.I.A.D.EP..LSSYVSVSAQSGV..AQRA
Retrocopy VFQQASYVVDVAENNPPGASIAQ<VSASDPDLGPNGQVSYSIVASDLEPGSLSSYVSVSAQSGVLFAQRA

Parental  F-HERLRAFELTLQAGDQGSPALSAHVSLRVLVGDRNDNAPRVLYPALGP
          F.H..LRAFELTLQA.DQGSPAL.A.V.LRVLVGDRNDNAPRVLYPALGP
Retrocopy FNHKQLRAFELTLQARDQGSPALGALVTLRVLVGDRNDNAPRVLYPALGP

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_867 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000008368	2 retrocopies	retro_mputfur_472, retro_mputfur_473,
Tarsius syrichta	ENSTSYG00000004901	2 retrocopies	retro_tsyr_692, retro_tsyr_867 ,
Xenopus tropicalis	ENSXETG00000032691	1 retrocopy	retro_xtro_64,