RetrogeneDB ID: retro_tbel_2999

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_126054:769..1676(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPH
• Ensembl ID: ENSTBEG00000014942
• Aliases: None
• Description: peripherin [Source:HGNC Symbol;Acc:9461]

Sequence

>retro_tbel_2999
CGGACAAAGGCCTGCGTGGAAGTGGAGCGCTATAACCTGCCCGAAGGACATCCATGAGCTTCCGGAGAAATTGCCAGGAG
GAGATGCTTCAGAGAGAGGAAGCCGAAAAGCACTCTGCAATCTTTCAGAAAGGATGTTGACAACGCTTCTTTGGCACGTC
TTGACCTTGAGCGCTAAGTGGAGTCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAACTACACGAAGAGGAAATTCAGGAG
CTGCAGGCCCAGATTCAGGAACAGCATGTCCAAATCGATATGGATGTTTCCAAGCCTGATCTTCACGGCTGCCCTGCGTG
ATGTCCGTCAGCAGTATGAAAGTGTGGCTGCCAAGAACCTTCAGGAGGCAGAAGAATGGTACAAGTCCAAGTTTGCTGAC
CTCTCAGAAGATGCTAACCACAACAACGATGCACTGCACCAGGTGAAGCAGGAGTCCAATGAGTACCGGTGGCAGGTGCA
GTCCCTCACCTGTGAAGTGGACGCGCTGAAAGGAACTAATGAATCCCTGGAACACCAGATGCGTGAAATGGAAGAGAACT
TTGCTGTTGAAGCTGCTAACTACCAAGACACCATTGGCCGCCTGCAGGATGAGATTCAGAACATGAAGGAAGAAATGGTT
CGCCACCTTCGTGAATACCAAGACCTGCTCAATGTTAAGATGGCTCTCGACATTGAGATTGCCACCTACAGGAAGCTGCT
GGAAGGCGAGGAGAGCAGGATTTCTCTGCCTCTTCCAAACTTCTCCTCCCTGAATCTGAGGGAAATTAATCTGGATTCAC
TCCCTCTGGTTGACACCCACTCAAAAAGAACACTTCTGATTAAGACGGTTGAAACTAGAGATGGACAGGTTATCAATGAA
ACTTCTCAGCACCACAACAATCTTGAA

Alignment

ORF - retro_tbel_2999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.77 %
• Parental protein coverage: 64.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RERDRVQVERDGLAE-DLAALKQRL-EEETRKREDAEHNLVLF-RKDVDDATLSRLELERKIESLMDEIE
          R....V.VER..L.E.D...L...L..EE...RE.AE.....F.RKDVD.A.L.RL.LER..ESL..EI.
Retrocopy RTKACVEVERYNLPE>DIHELPEKL>QEEMLQREEAEKHSAIF>RKDVDNASLARLDLER*VESLQEEIA

Parental  FLKKLHEEELRDLQVSVESQQVQQVEVEATVKPEL-TAALRDIRAQYESIAAKNLQEAEEWYKSKYADLS
          FLKKLHEEE...LQ.....Q.VQ........KP.L.TAALRD.R.QYES.AAKNLQEAEEWYKSK.ADLS
Retrocopy FLKKLHEEEIQELQAQIQEQHVQ-IDMDVS-KPDL>TAALRDVRQQYESVAAKNLQEAEEWYKSKFADLS

Parental  DAANRNHEALRQAKQEMNESRRQIQSLTCEVDGLRGTNEALLRQLRELEEQFALEAGGYQAGAARLEEEL
          ..AN.N..AL.Q.KQE.NE.R.Q.QSLTCEVD.L.GTNE.L..Q.RE.EE.FA.EA..YQ....RL..E.
Retrocopy EDANHNNDALHQVKQESNEYRWQVQSLTCEVDALKGTNESLEHQMREMEENFAVEAANYQDTIGRLQDEI

Parental  RQLKEEMARHLREYQELLNVKMALDIEIATYPKLLEGEESRISVPVHSFASLSLR-TTVPEVEPQDSHSR
          ...KEEM.RHLREYQ.LLNVKMALDIEIATY.KLLEGEESRIS.P...F.SL.LR..........D.HS.
Retrocopy QNMKEEMVRHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNFSSLNLREINLDSLPLVDTHSK

Parental  KMVLIKTIETRDGEVVTESQKEQHSELD
          ...LIKT.ETRDG.V..E.....H..L.
Retrocopy RTLLIKTVETRDGQVINET-SQHHNNLE

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_2999 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2999 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000011873	2 retrocopies	retro_tbel_4240, retro_tbel_4726,
Tupaia belangeri	ENSTBEG00000014942	1 retrocopy	retro_tbel_2999 ,