RetrogeneDB ID: retro_tbel_4113

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_67716:6871..8197(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000004854
• Aliases: None
• Description: None

Sequence

>retro_tbel_4113
ATGCGTGAGATCGTGCACATCCAGGCCGGCCAGTGCGGCAACCAGATCGGCGCCAAGTTTTGGGACGTTATCAGTGATGA
ACACGATATCGACCCCACTGACAGTTATCGTGGAGACAGTGATTTGCAGCTGGAAAGAATCAATGTGTACTACAATGAAG
CCACTGGTAACAAATACATGCCCCGGGCTATTCTGGTGGATCTGGAACCTGGCACCATGGACTCAGTGCGGTCTGGACCA
TTTGGCTAGATCTTCAGGCCAGACAACTTTGTGTTTGGCCAGAGTGGTGCTGGGAACAACTGGGCCAAGGGCCACTACAC
AGAGGGGGCCGAACTGGTCAACTCGGTCCTGGATGTGGTGAGGAAGGAGTCAGAAAGCTGTGACTGTCTCCAGGGCTTCC
AGCTGACCCACTCGCTGGGAGGTGGCACCGAGTCAGGCATGGGCATCCTGCTCATCAGCAAGATCCGTGAGGAGTACCGG
GACCACATCATGATCACCTTCAGCGTCATGCCCTCACCCAAGGTGTCTGACACGGTGGTGGAGCCCTACAACGCCACCCT
GTCCATGCACCAGCTGGTGGAGAACACTGACGAGTCCTACTGCATTGACAACGAGGCCCTGTACAACATCTGCTTCCGCA
CCCTGAAGCTGACCACACCCACCCACGGAGACCTCCACCACCTGGTGTCGGCCACCATGAGCGGCGTCACCACCTGCTTG
CGCTTCCCGGGCCAGCTGAATACCGACCTGCGCAAGCTGGCCGTGAACAGGTGCCCTTCCCGCGCCTGCACTTCTTCATG
CCTGGCTTCGCGCCCCTGACCAGCCGGGGCAGCCAGCAGTACGGCGCGCTCATGGTGCCCGAGCTCACCCAGCAGATGTT
CGACTCCAAGAACATGATGGTCGCAGGCCACGGCCACTACCTGACGGTGGCTGCCATCTTCTGAGGCCGCATGTCCATGA
AGGAGGTGTACGAGCAGATGCTCAACGTGCAGAACAAGGACAGCAGCTACTTCGTGGAAGTGGATCCCCAACAACGTCAA
GACGGCCGTGTGCGACATCCCACCTCGTGGCCTCCAGATGTCAGCCACCTTCATCGGCAACAGCACGGCCATCCAGGAGC
TGTTCAAGCGCATCTCGGAGCAGTTCACGGCCATGTTCCGGCGCAAGGCCTTCCTGCACAGGTACGCGGGCGAGGGCATG
GACGAGATGGAGTTCACCAAGGCCGAGAGCAACATGAACGACCTGGTGTCCAAGTACCAGCAGTGCCAGGACGCCACGGC
CGAGGAGCAGGGTGAGTTCGAGGAGGAGGAGGGTGAGGACGAGGCT

Alignment

ORF - retro_tbel_4113 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEP
          MREIVHIQAGQCGNQIGAKFW.VISDEH.IDPT.SY.GDSDLQLERINVYYNEATGNKY.PRAILVDLEP
Retrocopy MREIVHIQAGQCGNQIGAKFWDVISDEHDIDPTDSYRGDSDLQLERINVYYNEATGNKYMPRAILVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLG
          GTMDSVRSGPFG.IFRPDNFVFGQSGAGNNWAKGHYTEGAELV.SVLDVVRKESESCDCLQGFQLTHSLG
Retrocopy GTMDSVRSGPFG*IFRPDNFVFGQSGAGNNWAKGHYTEGAELVNSVLDVVRKESESCDCLQGFQLTHSLG

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          GGT.SGMG.LLISKIREEY.D.IM.TFSVMPSPKVSDTVVEPYNATLS.HQLVENTDE.YCIDNEALY.I
Retrocopy GGTESGMGILLISKIREEYRDHIMITFSVMPSPKVSDTVVEPYNATLSMHQLVENTDESYCIDNEALYNI

Parental  CFRTLKLTTPTYGDL-NLVSATMSGVTTCLRFPGQLNADLRKLAVN-MVPFPRLHFFMPGFAPLTSRGSQ
          CFRTLKLTTPT.GDL..LVSATMSGVTTCLRFPGQLN.DLRKLAVN..VPFPRLHFFMPGFAPLTSRGSQ
Retrocopy CFRTLKLTTPTHGDLHHLVSATMSGVTTCLRFPGQLNTDLRKLAVN<QVPFPRLHFFMPGFAPLTSRGSQ

Parental  QYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVE-WIPNN
          QY.AL.VPELTQQMFD.KNMM.A....HG.YLTVAA.F.GRMSMKEV.EQMLNVQNK.SSYFVE.WIPNN
Retrocopy QYGALMVPELTQQMFDSKNMMVA---GHGHYLTVAAIF*GRMSMKEVYEQMLNVQNKDSSYFVE>WIPNN

Parental  VKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDL
          VKTAVCDIPPRGL.MSATFIGNSTAIQELFKRISEQFTAMFRRKAFLH.Y.GEGMDEMEFT.AESNMNDL
Retrocopy VKTAVCDIPPRGLQMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHRYAGEGMDEMEFTKAESNMNDL

Parental  VSEYQQYQDATAEEEGEFEEEAEEEVA
          VS.YQQ.QDATAEE.GEFEEE..E..A
Retrocopy VSKYQQCQDATAEEQGEFEEEEGEDEA

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_4113 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4113 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 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017637	1 retrocopy	retro_cjac_1649,
Erinaceus europaeus	ENSEEUG00000002955	1 retrocopy	retro_eeur_441,
Myotis lucifugus	ENSMLUG00000016179	1 retrocopy	retro_mluc_401,
Tupaia belangeri	ENSTBEG00000004854	9 retrocopies	retro_tbel_2291, retro_tbel_3456, retro_tbel_3944, retro_tbel_4113 , retro_tbel_413, retro_tbel_4390, retro_tbel_4439, retro_tbel_961, retro_tbel_962,
Tarsius syrichta	ENSTSYG00000003440	2 retrocopies	retro_tsyr_1068, retro_tsyr_2125,
Tursiops truncatus	ENSTTRG00000006144	1 retrocopy	retro_ttru_1393,