RetrogeneDB ID: retro_tbel_4412

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_81576:2126..3298(-)
• 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_4412
AATGTGCTGATCTTCCACTTGGGAGGTGGCACGTTTGATGTGTCCATCCTCACTATGGAGGATGGAATTTTTGAGATCAA
ATCTACAGCTGGAGATACACACTTGGGCGGAGAAGACTTTGGCAATCGCATGGTCAACCGTTTCATCCCTGAATTTAAGT
GCAAGAATAAGAAGGACATCAGTGAGAATAAGAGAGCTGTCTGGTGCCTTTGCACTGCTTGTGAACGGGCTAAGCACACC
CTCTCCTCCAGCACCCAGGCCAATATTGAGATTGACTCCCTCTATGAAGGAATCAACTTCTATACCTGCATTACCCATGC
CTGATTTAAAGAATTGAACACAGACCTGTTCTGTGGAACCCTGGACCCTGTAGAGAAAGCCCTTCAGGATGCCAAACTAG
ACAAGTCACAGATCCATGACATCGTCCTGATGAGTGGCTCTACTCTTATTCCCAAGACTCAGAAGCTGCTACAAGACTTC
TTCAATGGAAAGGAACTGAAAAAGAGCATCAACCCTGATGAGGCTGTTGCTTATAGTGCAGCTGTCCAGGAAGCCGTCTT
ATTAGGAGACAAATCTGACAATGTCCAGGATCTGCTGCTCTTGGTATTCACTCCCCTCTCCCTTGGCATTGAAATGCTGG
CGGAGTCATGACTGTCTTCATCAATGTAATACCACCATTCCTACCAAGCAGACACAGACCTTCACGACCTACTCTGACAG
CCAGCCTGGTGTACTCATTTAGGTTAGGAAAGTGAATGTGCCATGACCAAGATACCAACCTGCTGGGCAAGTTTGAAATC
ACAGGGATACCTCCTGCACCCCTTGGTGTTCCTCAGATTAAAGTCACTTTCGATATTGATGCCAACGGCATCCTGAATGT
CTCTGCTGTGGATAAAAGTACTGGAAAAGAGAACAAGGTCACCATCACTAATGATAAGGGTCATCTGAGCAAGGAGGACA
TTGAGTGCATGGTCCAGGAAGCTGAGAAGTACAAGGCTGAAGACGAGAAGCAGAGGGACAAGGTGTCTTCCAAGAATTCA
CTAGAGTCTTACGCGTTCAACATGAAAGCAATGGTAGAAGATGAGAAACTTTAAGGCAAGATCAACGATGAGGATAAACA
GAAGACTCTTGACAAATGTAATGAAATCATCAACTGGCTTGACAAGAACCAG

Alignment

ORF - retro_tbel_4412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.86 %
• Parental protein coverage: 67.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRL
          NVLIF.LGGGTFDVSILT.EDGIFE.KSTAGDTHLGGEDF.NRMVN.FI.EFK.K.KKDISENKRAV..L
Retrocopy NVLIFHLGGGTFDVSILTMEDGIFEIKSTAGDTHLGGEDFGNRMVNRFIPEFKCKNKKDISENKRAVWCL

Parental  RTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHD
          .TACERAK.TLSSSTQA.IEIDSLYEGI.FYT.IT.A.F.ELN.DLF.GTLDPVEKAL.DAKLDKSQIHD
Retrocopy CTACERAKHTLSSSTQANIEIDSLYEGINFYTCITHA*FKELNTDLFCGTLDPVEKALQDAKLDKSQIHD

Parental  IVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGI
          IVL..GST.IPK.QKLLQDFFNGKEL.KSINPDEAVAY.AAVQ.A.L.GDKS.NVQDLLLL..TPLSLGI
Retrocopy IVLMSGSTLIPKTQKLLQDFFNGKELKKSINPDEAVAYSAAVQEAVLLGDKSDNVQDLLLLVFTPLSLGI

Parental  E-TAGGVMTVLI-KRNTTIPTKQTQTFTTYSDNQPGVLIQVY-EGERAMTK-DNNLLGKFELTGIPPAPR
          E..AGGVMTV.I...NTTIPTKQTQTFTTYSD.QPGVLI.V..E.E.AMTK.D.NLLGKFE.TGIPPAP.
Retrocopy E<NAGGVMTVFI<QCNTTIPTKQTQTFTTYSDSQPGVLI*VR<ESECAMTK<DTNLLGKFEITGIPPAPL

Parental  GVPQIEVTFDIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSK
          GVPQI.VTFDIDANGILNVSAVDKSTGKENK.TITNDKG.LSKEDIE.MVQEAEKYKAEDEKQRDKVSSK
Retrocopy GVPQIKVTFDIDANGILNVSAVDKSTGKENKVTITNDKGHLSKEDIECMVQEAEKYKAEDEKQRDKVSSK

Parental  NSLESYAFNMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQ
          NSLESYAFNMKA.VEDEKL.GKINDEDKQK.LDKCNEIINWLDKNQ
Retrocopy NSLESYAFNMKAMVEDEKL*GKINDEDKQKTLDKCNEIINWLDKNQ

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_4412 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4412 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,