RetrogeneDB ID: retro_tbel_4122

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_68011:3728..4675(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3B
• Ensembl ID: ENSTBEG00000011579
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) beta [Source:HGNC Symbol;Acc:5385]

Sequence

>retro_tbel_4122
ATGATGACACTGGGTGGAGTCCACTGGCTGATCTGGGTACAGGTCTCTGCCCCAAATCTTGGTTCATGAAGAGTACTGGG
TACTTTGGCCTCAGTGCATGGTACCACACAGCTAGACAAGGATATAAGGGGGAAGGTGCCTTTCTATTAGCCTTGCTGCC
CAGAGATAGCACGGGGCCTGAACTGATACACACCATCCAGGAGGTGTTCAGGTTGCTGCTGTCGTGGTGGAGTTCCAGGA
GTGCCACTTGAGTGAGGTGCAGAATATGGCATCGGAGGAGAAGCTGGCATGGGTGCTGAGTTTTAGGAAGGAAAATAAGG
TTGCCATCATTGGGAAGATCCATTCCTCAGTGGAGTATAAGGGAGAATTAGCCTTCAACAACATGTGGTAAGGCTTAAGT
TGGACTAGTTTGCCAATGTAGTTCACATGAAGTCACTTCCTGGGTACATGACTTGGCACAGTCATCTCGACCTGGTGATC
ATTCTAGAGCAGATAGAAAAGGAGTACATCACTCTGGAACATGAGAGTACAAGGAGCACAATCGAGTGCTTGAAGATTGC
CACTAGAGCCGAGTCTCAGCAGATTGTAAAGTTCACTTTTGGCTACGCCACCAAGAAAGGGCAGAGCAAAGACACAGCGG
TTCATTGGCCAACATGATGAAACTTTGGGATGGGTTGTCTTCTAGTCCTGTGAGGAACTTGCTGAACTGTACCCCCAAAT
CAAGTTTGAGATGAAGATCACAGATAATTGCTTATGTAACTGGTGCAGAATCCTTACCAGTCTGATGTGCTAGTGATGCC
CAGTCTCTGAGGGAACATTATTGACAACCTGACTCCTGGCCTGGTTGGGGGAGCTGGCATCGTCCCCGGTGACAGCTACA
GTGCAGAGTATGCAGTCTTTGAGTGGGCACCCAGCAACCATTTGCCCAGGCAGTGGTCAGAAACTTG

Alignment

ORF - retro_tbel_4122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.56 %
• Parental protein coverage: 82.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MAALSGVRWLTRALVPASNPGPWRSLGTSAAAHAATRSQAEDVRV-EGAFPVTMLPGDGVGPELMHAVKE
          M..L.GV.WL....V.A.N.G..R.LGT.A..H..T.....D.R..EGAF....LP.D..GPEL.H...E
Retrocopy MMTLGGVHWLIWVQVSAPNLGS*RVLGTLASVHGTTQLD-KDIRG<EGAFLLALLPRDSTGPELIHTIQE

Parental  VFK-AAAVPVEFQEHHLSEVQNMASEEKLEQVLSSMKENKVAIIGKIHTPMEYKGELASYDMR-LRRKLD
          VF...AAV.VEFQE.HLSEVQNMASEEKL..VLS..KENKVAIIGKIH...EYKGELA...M...R.KLD
Retrocopy VFR<VAAVVVEFQECHLSEVQNMASEEKLAWVLSFRKENKVAIIGKIHSSVEYKGELAFNNMW<VRLKLD

Parental  LFANVVHVKSLPGYMTRHNNLDLVIIREQTEGEYSSLEHESARGVIECLKIVTRAKSQRIAKFAFDYATK
          .FANVVH.KSLPGYMT.H..LDLVII.EQ.E.EY..LEHES.R..IECLKI.TRA.SQ.I.KF.F.YATK
Retrocopy *FANVVHMKSLPGYMTWHSHLDLVIILEQIEKEYITLEHESTRSTIECLKIATRAESQQIVKFTFGYATK

Parental  KGRSKVTAVH-KANIMKLGDGLFLQ-CCEEVAELYPKIKFETMIIDNC-CMQLVQNPYQFDVLVMPNLYG
          KG.SK.TAVH..AN.MKL.DGL.....CEE.AELYP.IKFE..I.DNC..M.LVQNPYQ.DVLVMP.L.G
Retrocopy KGQSKDTAVH<LANMMKLWDGLSSS<SCEELAELYPQIKFEMKITDNC<LM*LVQNPYQSDVLVMPSL*G

Parental  NIIDNLAAGLVGGAGVVPGESYSAEYAVFE-TGARHPFAQAVGRNI
          NIIDNL..GLVGGAG.VPG.SYSAEYAVFE..G...PFAQAV.RN.
Retrocopy NIIDNLTPGLVGGAGIVPGDSYSAEYAVFE<VGTQQPFAQAVVRNL

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_4122 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4122 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005208	1 retrocopy	retro_mdom_106,
Otolemur garnettii	ENSOGAG00000004684	1 retrocopy	retro_ogar_2890,
Sarcophilus harrisii	ENSSHAG00000017173	1 retrocopy	retro_shar_94,
Tupaia belangeri	ENSTBEG00000011579	2 retrocopies	retro_tbel_3404, retro_tbel_4122 ,