RetrogeneDB ID: retro_tbel_3907

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_3371:74654..75704(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPN1
• Ensembl ID: ENSTBEG00000007425
• Aliases: None
• Description: GPN-loop GTPase 1 [Source:HGNC Symbol;Acc:17030]

Sequence

>retro_tbel_3907
GTGTTGGGAATGGCAGGATCAGGAAAAAACACTTTTGCACACAGGCTAACACGATACCTGCATAGCCAGGGCTCTCCACC
TTATGTGATAAACCTAGACCCAGCTGTGCATGAAGTCCCATTTCTTGCCATTATTGAATTTCGTGACATTGTGAAGTATA
AAGAAGTCATGAAACAATATGGACTTGGACCCAATGGAGGCATAGTTACCTCACTCAATCTCTTTGCTACCAGATTTGAT
CAGGTGATAAAATTTGTGGAGAAAGCCCAGAACATACCTAAATATGTCTTGATTGACACACCTGGACAGATTGAGGTGTT
TTCCTGGTCAGCTTCTGGGACAACCATCACTGAGGCTTTGACATCCTCATTTCCAACAGTTGTCATCTATGTAATGGACA
CATCACAAAGTACCAACCCAGTGACATTCATGTTCAATATGCTCTATGCCTGTAGCATCTTGTACAAAACCAAGCTACCT
TTCATTGTGGTCATGAACAAAATTGACATCATTGATCACAGCTTTGCAGTGGAATGGATGCAGGATTTTGAGGCTTTCCA
AGATGCCATAAATCGAGAGACCACATATGTCAGTAACCTGACTTGTTCCAAGAGCCAGGTGTTAGATGAGTTTTACAGCT
CACTCAGGGTAGTGGGTGTGTCTGAAGTTCTGGGTACCAGTTTAAATGAACTCTTATGCAAATCACCAGTGCTGCAGAAG
AATATGAAAGGGAGTATCTCCCTGAACATGAACGTCTGAAGAAATCACTGGCCAGTGTGTAGAGCCAACAGCAGAAAGAG
CAACTAGAATGCCTTCGGAAAGGTATGGGTTCTGTAGCCTTGGTCATGGGGACTTCCAAAGACAGTGCATCCTCTGTGCT
AGACCCTTCTGACCTGATCCTGACTCAAAGAACCTGGATGAAGAGGATGAGGAGGCAGACAGTGATACTGATGACATTGA
CCACAGAGTTACAGAGGAGAGCCATGAAGAACCAACTTTCCAGAATTTTATGCAAAATCAATGGCATAATACTGGAAGAG
GAATAACAAA

Alignment

ORF - retro_tbel_3907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.31 %
• Parental protein coverage: 93.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLGMAGSGKTTFVQRLTGYLHSQGSPPYVINLDPAVHEVPFPANIDIRDTVKYKEVMKQYGLGPNGGIVT
          VLGMAGSGK.TF..RLT.YLHSQGSPPYVINLDPAVHEVPF.A.I..RD.VKYKEVMKQYGLGPNGGIVT
Retrocopy VLGMAGSGKNTFAHRLTRYLHSQGSPPYVINLDPAVHEVPFLAIIEFRDIVKYKEVMKQYGLGPNGGIVT

Parental  SLNLFATRFDQVMKFIEKAQNMSKYVLIDTPGQIEVFTWSASGTIITEALASSFPTVVIYVMDTSRSTNP
          SLNLFATRFDQV.KF.EKAQN..KYVLIDTPGQIEVF.WSASGT.ITEAL.SSFPTVVIYVMDTS.STNP
Retrocopy SLNLFATRFDQVIKFVEKAQNIPKYVLIDTPGQIEVFSWSASGTTITEALTSSFPTVVIYVMDTSQSTNP

Parental  VTFMSNMLYACSILYKTKLPFIVVMNKTDIIDHSFAVEWMQDFEAFQDALNQETTYVSNLTRSMSLVLDE
          VTFM.NMLYACSILYKTKLPFIVVMNK.DIIDHSFAVEWMQDFEAFQDA.N.ETTYVSNLT.S.S.VLDE
Retrocopy VTFMFNMLYACSILYKTKLPFIVVMNKIDIIDHSFAVEWMQDFEAFQDAINRETTYVSNLTCSKSQVLDE

Parental  FYSSLRVVGVSAVLGTGLDEL-FVQVTSAAEEYEREYRPEYERLKKSLASAQSQQQKEQLERLRKDMGSV
          FYSSLRVVGVS.VLGT.L.EL...Q.TSAAEEYEREY.PE.ERLKKSLAS..SQQQKEQLE.LRK.MGSV
Retrocopy FYSSLRVVGVSEVLGTSLNEL<LMQITSAAEEYEREYLPEHERLKKSLASV*SQQQKEQLECLRKGMGSV

Parental  ALDTGTSKDS-HTLWDLSDLILTRGT-LDEEDEEADSDTDDIDHRVTEESHEEPAFQNFMQ-ESMAQYWK
          AL..GTSKDS.....D.SDLILT..T.LDEEDEEADSDTDDIDHRVTEESHEEP.FQNFMQ..SMA.YWK
Retrocopy ALVMGTSKDSASSVLDPSDLILTQRT<LDEEDEEADSDTDDIDHRVTEESHEEPTFQNFMQ<KSMA*YWK

Parental  RNNK
          RNNK
Retrocopy RNNK

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_3907 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3907 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013421	1 retrocopy	retro_eeur_146,
Microcebus murinus	ENSMICG00000014941	1 retrocopy	retro_mmur_649,
Ictidomys tridecemlineatus	ENSSTOG00000006379	2 retrocopies	retro_itri_1428, retro_itri_1718,
Tupaia belangeri	ENSTBEG00000007425	1 retrocopy	retro_tbel_3907 ,