RetrogeneDB ID: retro_tbel_3644

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_147802:51038..52283(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000001566
• Aliases: None
• Description: None

Sequence

>retro_tbel_3644
TTCGGCCTGCAGTATGATCTTGAAGGCCATGTTGGTTGTGTGAATACTGTGCACTTTAACCAGCGTGGCACCTGGCTAGC
CAGTAGTGGTGACGACCTGAAGGTGATAGTGTGGGACTGGACACGGCAGCAAGCATTGCTGACCTTTGAGAGTGGCCACA
GAAATAATGTCTTTCAGGCTAAATTCCTTCCTAATTGTGGTGATTCCATCCTGGCCATGTGTGCCCGTGATGGGCAGGTA
CGGGTAGCAGAACTGTCTGCTACACCACACTGCAAGAATACCAAGCATGTGGCTCAGCATGGAGGAGCTTCACATAAGTT
GGCTTTAGATCCAAGCTCCCCCTTTACATTCCTAACTTCAGGTGAAGATGCAGTTGTCTTCACCATTGACCTCAGAAAAG
AGCAGCCAGCTAGGAAAATGTTGGTAATAAAAGAGGAGGAGAAGAAAGTGGGACTGTATACAATCTGTGTGAATCCTGCT
GATACCTACCAGTTTGCAGTAGGTGGACAAGATCAGTTTGTAAGGATTTATGATCAGAGGAAGACTGGTGAAAATGAGAA
CAGTGGAGTACTCAAGAAATTTTGTCCTCATCACTTGTTGGGCTATGATTCCAATGTAAGCATCACCTGCCTTGTGTACA
GCCATGATGGAACAGAACTTCTGGCCAGCTACAATGATGAAGATATTTACCTCTTTAACTCCGCCCATGATGATGGAGCT
CAATATGTTAAAAGATATAAGGGACACAGAAATAATGCCACAGTCAAAGGCGTCAATTTCTATGGCCCCAGAAGTGAGTT
TGTGGTGAGCGGCAGTGATTGTGGTCACATCTTCCTCTGGGAGAAGTCATCCTGCCAGATAATTCAGTGCCTGGATGGAG
ACAAAGGAGGTACTATAAACTGTCTTGAGCCTCACCCTTACCTACCTATGATGGCAACCAGTGGCCTAGACCATGATGTC
AAGATCTGGGCACCCACAGCAAAAGGTTCCACTGACCTCACCTGGTTGAAAAATGTGATTAACAGGAACAAGCGGAAACG
AGATGAAGATAATTTGCACCATGCTACCTTGTATGATAACCACTTGCTTTGGTTCCTCATGCATCACCTGACACAGAGTG
ATCCTGACCAGGATGAGGGAGGACCTGAAGATGAAGACCTAGATGCAGATTCAAATGAGTTTTCCAGCACCTCAGATACA
GCCGAGGAAGAAGAAAGCGAAGACCATGTGCAGTGCTTGCCATCC

Alignment

ORF - retro_tbel_3644 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.77 %
• Parental protein coverage: 69.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FRLQHGLEGHTGCVNTLHFNQRGTWLASGSDDLKVVVWDWVRRQPVLDFESGHKSNVFQAKFLPNSGDST
          F.LQ..LEGH.GCVNT.HFNQRGTWLAS..DDLKV.VWDW.R.Q..L.FESGH..NVFQAKFLPN.GDS.
Retrocopy FGLQYDLEGHVGCVNTVHFNQRGTWLASSGDDLKVIVWDWTRQQALLTFESGHRNNVFQAKFLPNCGDSI

Parental  LAMCARDGQIRVAELSAT-QCCNTKRV-QHRGASHKXXXXXXXXCTFLSAEEDAVVFTIDLRQDRPASKL
          LAMCARDGQ.RVAELSAT..C.NTK.V.QH.GASHK.........TFL...EDAVVFTIDLR...PA.K.
Retrocopy LAMCARDGQVRVAELSATPHCKNTKHVAQHGGASHKLALDPSSPFTFLTSGEDAVVFTIDLRKEQPARKM

Parental  VVTKEKEKKVGLYTIYVNPANTHQFAVGGRDQFVRIYDQRKIDENENNGVLKKFCPHHLVNSESKANITC
          .V.KE.EKKVGLYTI.VNPA.T.QFAVGG.DQFVRIYDQRK..ENEN.GVLKKFCPHHL....S...ITC
Retrocopy LVIKEEEKKVGLYTICVNPADTYQFAVGGQDQFVRIYDQRKTGENENSGVLKKFCPHHLLGYDSNVSITC

Parental  LVYSHDGTELLASYNDEDIYLFNSSHSDGAQYVKRYKGHRNNATVKGVNFYGPKSEFVVSGSDCGHI-LW
          LVYSHDGTELLASYNDEDIYLFNS.H.DGAQYVKRYKGHRNNATVKGVNFYGP.SEFVVSGSDCGHI.LW
Retrocopy LVYSHDGTELLASYNDEDIYLFNSAHDDGAQYVKRYKGHRNNATVKGVNFYGPRSEFVVSGSDCGHIFLW

Parental  EKTSCQIVQFMEGDKGXXVNCLEPHPHLPVLATSGLDHDVKIWAPTAEASTELTGLKEVIKKNKRERDED
          EK.SCQI.Q...GDKG...NCLEPHP.LP..ATSGLDHDVKIWAPTA..ST.LT.LK.VI..NKR.RDED
Retrocopy EKSSCQIIQCLDGDKGGTINCLEPHPYLPMMATSGLDHDVKIWAPTAKGSTDLTWLKNVINRNKRKRDED

Parental  SLHQTDLFDSHMLWFLMHHLRQRRHHRRWREPGVGATDADSDESPSSSDTSDEEEGPDRVQCMPS
          .LH...L.D.H.LWFLMHHL.Q.........P.....DADS.E..S.SDT..EEE..D.VQC.PS
Retrocopy NLHHATLYDNHLLWFLMHHLTQSDPDQDEGGPEDEDLDADSNEFSSTSDTAEEEESEDHVQCLPS

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3644 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3644 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014293	1 retrocopy	retro_amel_47,
Bos taurus	ENSBTAG00000005796	1 retrocopy	retro_btau_1853,
Canis familiaris	ENSCAFG00000031010	1 retrocopy	retro_cfam_223,
Callithrix jacchus	ENSCJAG00000005913	1 retrocopy	retro_cjac_1322,
Echinops telfairi	ENSETEG00000012876	1 retrocopy	retro_etel_654,
Felis catus	ENSFCAG00000003925	1 retrocopy	retro_fcat_14,
Mustela putorius furo	ENSMPUG00000013949	1 retrocopy	retro_mputfur_173,
Mus musculus	ENSMUSG00000026554	1 retrocopy	retro_mmus_111,
Otolemur garnettii	ENSOGAG00000011349	1 retrocopy	retro_ogar_2113,
Pteropus vampyrus	ENSPVAG00000007982	1 retrocopy	retro_pvam_1356,
Sus scrofa	ENSSSCG00000006388	1 retrocopy	retro_sscr_88,
Tupaia belangeri	ENSTBEG00000001566	1 retrocopy	retro_tbel_3644 ,