RetrogeneDB ID: retro_tbel_107

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1163:212062..213544(+)
• Located in intron of: ENSTBEG00000008054

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS45
• Ensembl ID: ENSTBEG00000010744
• Aliases: None
• Description: vacuolar protein sorting 45 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14579]

Sequence

>retro_tbel_107
GAGAATGTGGATTATCTGATTCAGGAACTCCGAAGACCCAAATACAGTATATATTTTATTTATTTCAGTAATGTGATCAG
CAAGAGTGACATGAAGTCGTTGGCTGAAGCTGATGAACAGGAAGTTGTGGCTGAGGTTCAGGAATTTTATGGTGATTACA
TTGCTGTGAATCCACACTTGTTTTCCCTCAATATTTTGGGTTGCTGCCAGGGTCGCAATTGGGATCCAGCCCAGCTATCC
AGAACAACTCAAGGACTGAAAGCTCTCCTTTTATCTCTGAAGAAGTGTCCTATAATTCGTTATCAGCTTGCATCAGAGGC
AGCCAAGAGACTTGCAGAATGTGTTAAGCAAGTGATAACTAAAGAATACGAGCTCTTTGAATTTCAGCGGACAGAAGTCC
CTCCATTGCTGCTTATTTTAGATCACTGTGATGATGCCATCACCCCATTGCTAAACCAGTGGACGTACCAGGCCATGGTC
CACGAACTACTAGGTATAAACAACAATCACATCAATCTCTCCAGAGTGCCGGGAATCAGTAAAGACTTAAGAGAGGTGGT
CCTGTCTGCTGAAAATGATGAGTTCTATGCTAATAATATGTACCTGAACTTTGCTGAGCTTGGTAGCAATATAAAGAATC
TCATGGAAGACTTTCAAAAGAAGAAACCAAAAGAACAGCAAAAACTAGAATCAAGAGCAGACATGAAGGCCTTTGTTGGG
AACTATCCACAGTTTAAGAAGATGTCTGGAACTGTATCAAAGCACGTGACTGTGGTTGGAGAACTGTCTCGGTTGGTCAG
TGAGCGGAATCTGCTAGAGGTTTCAGAAACTGAGCAAGAACTAGCCTGTCAAAATGATCATTCCAGTGCTCTCCAGAATG
TAAAGAGGCTCCTGCAGAACCCCAAAGTGACAGAGTTTGACGCTGCCCGCCTGGTGATGCTCTACGCTCTGCATTATGAG
AGACACAGCAGCAACCACCTGCCAGGACTCATGATGGACCTCAGGAATAAAGGTGTTTCAGAGAAGTATCGAAAGCTTGT
GTCTGCACTTGTTGAATATGGTGGTAAACGAGTCAGAGGAAGTGACCTCTTCAGCCCCAAAGATGCTGTGGCTATCACCA
AACAGTTCCTCAAAGGCCTGAAGGGAATAGAAAATGTGTACACACAGCACCAGCCGTTCCTGCATGAGACCCTGGACCAC
CTCATCAAAGGCAAGCTGAAGGAAAACCTGTACCCTTATCTAGGCCCCAGCACGCTCAGAGACAGACCTCAGGATATCAT
TGTGTTCGTAATTGGAGGGGCCACCTATGAAGAGGCTCTGACCGTTTATAACCTGAACCGAACCACGCCTGGAGTAAGGA
TTGTCCTGGGTGGAACCACGATACACAATATGAAAACTTTCCTAGAGGAAGTTCTGACCTCTGGACTGCACAGCCGGAGC
AGGGAGAGCACCCAAGCCACGTCGAGGTCGGTGAGCAGGAGA

Alignment

ORF - retro_tbel_107 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.75 %
• Parental protein coverage: 86.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENVDYLIQELRRPKYSIYLMYFSNVISKSDVKSLAEADEQEVVAEVQEFYGDYIAVNPHLFSLNILGCCQ
          ENVDYLIQELRRPKYSIY..YFSNVISKSD.KSLAEADEQEVVAEVQEFYGDYIAVNPHLFSLNILGCCQ
Retrocopy ENVDYLIQELRRPKYSIYFIYFSNVISKSDMKSLAEADEQEVVAEVQEFYGDYIAVNPHLFSLNILGCCQ

Parental  GRNWDPTQLSRTTQGLTALLLSLKKCPMIRYQLASEAAKRLAECVKQVITKEYELFEFRRTEVPPLLLIL
          GRNWDP.QLSRTTQGL.ALLLSLKKCP.IRYQLASEAAKRLAECVKQVITKEYELFEF.RTEVPPLLLIL
Retrocopy GRNWDPAQLSRTTQGLKALLLSLKKCPIIRYQLASEAAKRLAECVKQVITKEYELFEFQRTEVPPLLLIL

Parental  DRCDDAITPLLNQWTCQ-MVHALLGINNNRIDLSRVPGISKDLREVVLSAENDEFYANNMYLNFAEIGSN
          D.CDDAITPLLNQWT.Q.MVH.LLGINNN.I.LSRVPGISKDLREVVLSAENDEFYANNMYLNFAE.GSN
Retrocopy DHCDDAITPLLNQWTYQAMVHELLGINNNHINLSRVPGISKDLREVVLSAENDEFYANNMYLNFAELGSN

Parental  IKNLMEDFQKKKPKEQQKLESIADMKAFVENYPQFKKMSGTVSKHVTVVGELSRLVSERNLLEVSETEQE
          IKNLMEDFQKKKPKEQQKLES.ADMKAFV.NYPQFKKMSGTVSKHVTVVGELSRLVSERNLLEVSETEQE
Retrocopy IKNLMEDFQKKKPKEQQKLESRADMKAFVGNYPQFKKMSGTVSKHVTVVGELSRLVSERNLLEVSETEQE

Parental  LACQNDHSSALQNVKRLLQNPKVTEFDAARLVMLYALHYERHSSNSLPGLMMDLRNKGVSEKYRKLVSAV
          LACQNDHSSALQNVKRLLQNPKVTEFDAARLVMLYALHYERHSSN.LPGLMMDLRNKGVSEKYRKLVSA.
Retrocopy LACQNDHSSALQNVKRLLQNPKVTEFDAARLVMLYALHYERHSSNHLPGLMMDLRNKGVSEKYRKLVSAL

Parental  VEYGGKRVRGSDLFSPKDAVAITKQFLKGLKGVENVYTQHQPFLHETLDHLIKGKLKENLYPYLGPSTLR
          VEYGGKRVRGSDLFSPKDAVAITKQFLKGLKG.ENVYTQHQPFLHETLDHLIKGKLKENLYPYLGPSTLR
Retrocopy VEYGGKRVRGSDLFSPKDAVAITKQFLKGLKGIENVYTQHQPFLHETLDHLIKGKLKENLYPYLGPSTLR

Parental  DRPQDIIVFVIGGATYEEALTVYNLNRTTPGVRIVLGGTTIHNTKSFLEEVLTSGLHSRSRESTQATSRS
          DRPQDIIVFVIGGATYEEALTVYNLNRTTPGVRIVLGGTTIHN.K.FLEEVLTSGLHSRSRESTQATSRS
Retrocopy DRPQDIIVFVIGGATYEEALTVYNLNRTTPGVRIVLGGTTIHNMKTFLEEVLTSGLHSRSRESTQATSRS

Parental  VSRR
          VSRR
Retrocopy VSRR

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_107 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_107 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000501	1 retrocopy	retro_chof_1315,
Tupaia belangeri	ENSTBEG00000010744	1 retrocopy	retro_tbel_107 ,
Tursiops truncatus	ENSTTRG00000005060	1 retrocopy	retro_ttru_1807,