RetrogeneDB ID: retro_tbel_4610

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_93038:4585..5489(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000000496
• Aliases: None
• Description: None

Sequence

>retro_tbel_4610
TTCTCTTATGATGAAGCTTTTGCTATGGCTAATGACCCCTTGGCAGGCTTCCATGTAGTAAACCTTGCTCCACCCACATC
TCCGGACCTTCTTGGTGTGTGTGAAGCAGGAACACAAGAGCAGACTACATCGCCAAGTGTCATTTACCGGCCACATCCTT
CAGTTTATGCTCTACCCACAGCCAGGCTAATACCTTAGATGTTTCTGACCTTCCTACACAACGCGTGTATTCATCTCCCA
GACATTGAAATTGTGCAGAAATATCTAGTATCAGCATTCATGTTAGAGACTCAGCATCTTCTTCTACCTCTTGAATCACA
GCTGGGTTAACTAAGTTCACTCCGCAAAAGGACAACTGTAACGCAGAGAGGGAGTTTTTGCAGGTGCTACTGTAACAGAG
GCTTGTGATGGCAGTGATGATATTTTTGGGTTGAGTACTGATAGACTGTCCAAATTGTGAAGTCCATCTGTTTTGGACAT
CAGAGAAAAGGGCTATGAAAGAGTAAGAGAACTTGCAAAAGCTCAGAGGGAACTGAAGTTAAAAGATGAAGAATGTGAGA
GACTTTCAAAAGTATGAGATCAACTTGGACAGGAATTGGAAGAACTCACAGCTACTCTGTTTGAGGAAGCTCACAAAATG
GTGAGAGAAGCAAATGTCAAGCAGGCTACAGCAGAAGAGCAGTTAAAAGAAGCACAAGGAAAAACTGACGTACTTCAAGC
TGAGGTAGCTGCACTGAAGACACTGGTGTCCAGTTCTCCAACATGACCTACACGAGAGCCTCTGGCGGGTGGAAAGACAC
CTTTTAAAAACGGGCATACCAGAAATAAAAGTACAAGCAGAGCCATGAGTGGCAGCCTTCAGGACCTCAGTGTGATACAG
CCCATTGTAAAAGAGTGCAAAGAG

Alignment

ORF - retro_tbel_4610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.6 %
• Parental protein coverage: 64.96 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FSYDEAFAMANDPLEGFHEVNLASPTSPDLLSVYEAGTQEQTTSPSVIYRPHPS-ALCSAHIQANALDVS
          FSYDEAFAMANDPL.GFH.VNLA.PTSPDLL.V.EAGTQEQTTSPSVIYRPHPS..LCS.H.QAN.LDVS
Retrocopy FSYDEAFAMANDPLAGFHVVNLAPPTSPDLLGVCEAGTQEQTTSPSVIYRPHPS<SLCSTHSQANTLDVS

Parental  DLPTQPVYSSPRHLNCAEISGISIHVTDSAPSSTSGVTAGLTKLTTKKDNCNAEREFLQ-GATVTEACDG
          DLPTQ.VYSSPRH.NCAEIS.ISIHV.DSA.SSTS..TAGLTK.T..KDNCNAEREFLQ.GATVTEACDG
Retrocopy DLPTQRVYSSPRH*NCAEISSISIHVRDSASSSTS*ITAGLTKFTPQKDNCNAEREFLQ<GATVTEACDG

Parental  SDDIFGLSTDSLSRLRSPSVLEVREKGYERLKEELAKAQRELKLKDEECERLSKVRDQLGQELEELTASL
          SDDIFGLSTD.LS.L.SPSVL..REKGYER...ELAKAQRELKLKDEECERLSKV.DQLGQELEELTA.L
Retrocopy SDDIFGLSTDRLSKL*SPSVLDIREKGYERVR-ELAKAQRELKLKDEECERLSKV*DQLGQELEELTATL

Parental  FEEAHKMVREANVKQATAEKQLKEAQGKIDVLQAEVAALKTLVLSSSPTSPTQEPLPGGKTPFKKGHTRN
          FEEAHKMVREANVKQATAE.QLKEAQGK.DVLQAEVAALKTLV.SSSPT.PT.EPL.GGKTPFK.GHTRN
Retrocopy FEEAHKMVREANVKQATAEEQLKEAQGKTDVLQAEVAALKTLV-SSSPT*PTREPLAGGKTPFKNGHTRN

Parental  KSTSSAMSGSHQDLSVIQPIVKDCKE
          KSTS.AMSGS.QDLSVIQPIVK.CKE
Retrocopy KSTSRAMSGSLQDLSVIQPIVKECKE

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_4610 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4610 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000000496	1 retrocopy	retro_tbel_4610 ,