RetrogeneDB ID: retro_tbel_3524

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_143691:48869..49977(-)
• 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_3524
AACTTGGGAGGTGGCACTTTGACATGTCCATCCTCAATTGAGGATGGGATTTTTTTAGGTCAAATCTACAGCTGGAGATA
CACACTTGGGCGGAAAAGACTTCGACAATCGCATGGTCAACCATTTCATCACCGAGTTTAAGCGCAAGCATATGAAGGAC
ATCAGTGAGAACAAAAGAGCTGTCCGCCACCTTCACACTGCTTGTGAATGGGCTAAGCGCACCCTCTCCTCTAGCACCCA
GGCCAGTATTGAGATCAACACCCCCTATGAAGGAATCGACTTCTATACCTCCATTACCCGTGCCCGATTTGAAGAGTTGA
ATGTAGACGTGTTCTGTGGGCCCCTGGACCCTGTAGAGAAAGCCCTTCGGGACACCAAGCTAGACAAGTCACAGATCCAT
GACATTGTCCTGGTGAGTGGCTCTACTCTTATCCCCAAGATTCAGAAACTGCTACAAGACTTCTTCAATGGGAAGGAACT
GAATAAGAGCATCAACCCTGATGAGGCTGTTGTTTACGGAGCAGATGTCCAGGCAGCCATCTTATCTGGAGATAAGTCAA
GGACATCCAGGACCTGCTGCTCTTGGATGTCACGCCTCTGTCCCTCGGCATCGAAACTGCTGGCAGGGTCATGACTGTCC
TCATCAAGTGGAACACCACCATCCCTATCAAGTAGATGCAGACCTTCACCACCTACTCTGACAACCAGCCTGGGGTGCTC
ATCCAATTTTATGAAGGTGAGTGCACCATGACCAGGGATAACAACCTGCTGGGCAAGTTTGAGCTCACAGGCATACCTCC
TGCACCCCGTGGTGTTCCTCAGATTGAAGTCACTTTCGACATCGGTGCCAATGGCATCCTGAACGTCTCTTCTGTGGATA
AGAGTATCGGGAAAGAGAACAAGATCACCATCGCCAACGATAAGGGTCAGTCATCTGAGCAAGGAGGGCATTGAGCGCAT
GGTCCAGGAGGCTGAGAAGTACAAGGCTGAGGACGAGAAGGAGAGGGACAAGGTGTCTTCCAAGAACTCCCTGGAGTCCT
ACACGTTCAACATGAAAGCGACGGTGGAGAACGAGAACCTCCAAGGCAAGATCAATGATGAGGACAAG

Alignment

ORF - retro_tbel_3524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.38 %
• Parental protein coverage: 63.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLGGGTFDVSILTIEDGIFE-VKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTAC
          .LGGGT.......IEDGIF..VKSTAGDTHLGG.DFDNRMVNHFI.EFKRKH.KDISENKRAVR.L.TAC
Retrocopy NLGGGTLTCPS-SIEDGIFL>VKSTAGDTHLGGKDFDNRMVNHFITEFKRKHMKDISENKRAVRHLHTAC

Parental  ERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLV
          E.AKRTLSSSTQASIEI...YEGIDFYTSITRARFEELN.D.F.G.LDPVEKALRD.KLDKSQIHDIVLV
Retrocopy EWAKRTLSSSTQASIEINTPYEGIDFYTSITRARFEELNVDVFCGPLDPVEKALRDTKLDKSQIHDIVLV

Parental  GGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKS-ENVQDLLLLDVTPLSLGIETA
          .GST.IPKIQKLLQDFFNGKELNKSINPDEAV.YGA.VQAAILSGDKS....QDLLLLDVTPLSLGIETA
Retrocopy SGSTLIPKIQKLLQDFFNGKELNKSINPDEAVVYGADVQAAILSGDKS<KDIQDLLLLDVTPLSLGIETA

Parental  GGVMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEV
          G.VMTVLIK.NTTIP.K..QTFTTYSDNQPGVLIQ.YEGE..MT.DNNLLGKFELTGIPPAPRGVPQIEV
Retrocopy GRVMTVLIKWNTTIPIK*MQTFTTYSDNQPGVLIQFYEGECTMTRDNNLLGKFELTGIPPAPRGVPQIEV

Parental  TFDIDANGILNVSAVDKS-TGKENKI-TITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLES
          TFDI.ANGILNVS.VDKS..GK.......T.....LSKE.IERMVQEAEKYKAEDEK.RDKVSSKNSLES
Retrocopy TFDIGANGILNVSSVDKS>SGKRTRSPSPTIRVSHLSKEGIERMVQEAEKYKAEDEKERDKVSSKNSLES

Parental  YAFNMKATVEDEKLQGKINDEDK
          Y.FNMKATVE.E.LQGKINDEDK
Retrocopy YTFNMKATVENENLQGKINDEDK

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_3524 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3524 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,