RetrogeneDB ID: retro_tbel_4348

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_77961:2971..4127(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000011602
• Aliases: None
• Description: None

Sequence

>retro_tbel_4348
ACTTGGGAGGTGGCACTTTTGACGTGTCCATCCTCAATTGAGGATGGGATTTTTGAGGTCAAATCTACAGCTGGAGATAC
ATACTTGGGCAGAGAAGGCTTCGACTATCGCATGGTCAACCATTTCATTGCCGAGTTTAAGCGCAAGCATAAGAAGGACA
TCAGTGAGAACAAAAGAGTTGTCCGCCGCCTTCAAACTGCTTGTGAATGGGCTAAGCGCACCCTCTCCTCCAGCACCCAG
GCCAGTATTGAGATCAACACCCTCTATGAAGGAATCGACTTCTATACCTCCATTACCCATGCCCGATTTGAAGAGTTGAA
TGTAGACATGTTCCATGGGACCCTGGACCCTGTAGAGAAAGCCATTCGGGATGCCAAATTAGACAAGTCACAGATCCATG
ACATTGTCCTGGTGGGTGGCTCTACTCCTATCCCCAAGATTCAGAAACTGCTACAAGACTTCTTCAATGGGAAGGAACAG
AATAAGAGCATCAACCCTGATGAGGCTGTTGTTTACGGAGCAGATGTCCAGGCAGCCATCTTATCTGGAGATAAGTCAAG
GACATCCAGGACCTGCTGCTCTTGGATGTCACGCCTCTGTCCCTCGGCATCGAAATTGCTGGCGGGGTCATGACTGTCCT
CATCAAGTGGAACACCACCATCCCTATCAAGTAGATGCAGACCTTCACCACCTACTCTGACAACCAGCCTGGGGTGCTCA
TCCAGTTTTATGAAGGTGAGTGCACCATGATCAAGGATAACAACCTGCTGGGCAAGTTTGAGCTCACAGGCATACCTCCT
GCACCCCGTGGTGTTCCTCAGATTGAAGTCACTTTTGACATTGGTGCCAATGGCATCCTGAACGTCTCTGCTGTGGATAA
GAGTATCGGGAAAGAGAACAAGATCACCATCGCCAACGATAAGGGTCACCTGAGCAAGGAGGGCATCGAGCTCATGGTCC
AGGAGGCTAAGAAGTACAAGGTTGAGGACGAGAAGCAAAGGGACAAGGTGCCTTCCAAGAACTCCCTGGAGTTCTACGCA
TTCAACATGAAAGCCATGGTGAAGGACAAGAAACTCCAAGGCAAGATTAATAATGAGGACAAGCAGAAGATTCATGACAA
ATATATAAAATCATCAACTGGCTTGACAGAACCAGA

Alignment

ORF - retro_tbel_4348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.28 %
• Parental protein coverage: 65.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TFDVSILT----IEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACER
          T..V..LT....IEDGIFEVKSTAGDT.LG.E.FD.RMVNHFIAEFKRKHKKDISENKR.VRRL.TACE.
Retrocopy TWEVALLTCPSSIEDGIFEVKSTAGDTYLGREGFDYRMVNHFIAEFKRKHKKDISENKRVVRRLQTACEW

Parental  AKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGG
          AKRTLSSSTQASIEI..LYEGIDFYTSIT.ARFEELN.D.F.GTLDPVEKA.RDAKLDKSQIHDIVLVGG
Retrocopy AKRTLSSSTQASIEINTLYEGIDFYTSITHARFEELNVDMFHGTLDPVEKAIRDAKLDKSQIHDIVLVGG

Parental  STRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKS-ENVQDLLLLDVTPLSLGIETAGG
          ST.IPKIQKLLQDFFNGKE.NKSINPDEAV.YGA.VQAAILSGDKS....QDLLLLDVTPLSLGIE.AGG
Retrocopy STPIPKIQKLLQDFFNGKEQNKSINPDEAVVYGADVQAAILSGDKS<KDIQDLLLLDVTPLSLGIEIAGG

Parental  VMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTF
          VMTVLIK.NTTIP.K..QTFTTYSDNQPGVLIQ.YEGE..M.KDNNLLGKFELTGIPPAPRGVPQIEVTF
Retrocopy VMTVLIKWNTTIPIK*MQTFTTYSDNQPGVLIQFYEGECTMIKDNNLLGKFELTGIPPAPRGVPQIEVTF

Parental  DIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFN
          DI.ANGILNVSAVDKS.GKENKITI.NDKG.LSKE.IE.MVQEA.KYK.EDEKQRDKV.SKNSLE.YAFN
Retrocopy DIGANGILNVSAVDKSIGKENKITIANDKGHLSKEGIELMVQEAKKYKVEDEKQRDKVPSKNSLEFYAFN

Parental  MKATVEDEKLQGKINDEDKQKILDK-CNEIINWLDKNQ
          MKA.V.D.KLQGKIN.EDKQKI.DK....IINWLD...
Retrocopy MKAMVKDKKLQGKINNEDKQKIHDK<IYKIINWLDRTR

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_4348 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4348 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000012704	1 retrocopy	retro_eeur_8,
Microcebus murinus	ENSMICG00000004702	1 retrocopy	retro_mmur_7,
Sorex araneus	ENSSARG00000000161	1 retrocopy	retro_sara_31,
Tupaia belangeri	ENSTBEG00000011602	8 retrocopies	retro_tbel_1764, retro_tbel_344, retro_tbel_3488, retro_tbel_3524, retro_tbel_4348 , retro_tbel_4412, retro_tbel_4490, retro_tbel_471,