RetrogeneDB ID: retro_tbel_3774

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_15151:42112..42886(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSTBEG00000007755
• Aliases: None
• Description: fibrillarin [Source:HGNC Symbol;Acc:3599]

Sequence

>retro_tbel_3774
TTCCAGTCTGGTGGCAACCGGGGTCGCGGTCGGGGCGGAAAAAGAAGAAACCAGTCAGGGAAGAATGTAATGGTGGAACC
TCAACAGCATGAGAGTGTCTTCATCTGTGGAGGAAAGGAACATGCACTGGTCGCCAAAAACCTGGTCCCTGGAGAGTCAG
TTTATGGAGAGAAGAGAGTCTCAATTGCGGAGGGAGATGATAAAATCGAATACCGAGCCTGGAATCCCTTCAGCTCCAAG
CTGGTGGCAGCAATCCTGGGCGGCGTGGACCAGATCCACATCAAGCTAGGAGCCAAGGTGCTCTACCTCGGGGCTGCCTC
AGGCACCACTGTCTCCCACGTCTCTAACATTGTAGGCCCAGATGGTCTGGTCTATGCAGTCGAGTTCTCCCGCCACTCTG
GCCATGACCTCATTAACTTGGCCAAGAAAAGAACCAACATCATTCCTGTGATCGAGGATGCTCGGCACCCACACAAATAC
TGCATGCTCATCGCAATGGTGGATGTGATCTTTGCTGATGTGGCCCTGCCAGACCAGACCAGAATCGTGGCCCTGAATAC
CCACACTCTCCTGCGTAATGGAGGACACTTTGTGATTTCCATTAAGGCCAACTGCATGAACTCCACAGCCTCAGCAGAGG
CAGTGTTTGCTTCTGAAGTAAAAAAGATGCAGCAAGAGAACATGAAGGCCCAGGAGCAGTTGACCCTAGAGCCTTATGAG
AGAGACCATGCTGTGGTCGTGGGTGTGTACAGGCCACACCACAAGGTGAAGAAC

Alignment

ORF - retro_tbel_3774 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.7 %
• Parental protein coverage: 80.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FQSGGNRGRGRGGKKGNQSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSIAEGDDKIE
          FQSGGNRGRGRGGK..NQSGKNVMVEP..HE.VFIC.GKE.ALV.KNLVPGESVYGEKRVSIAEGDDKIE
Retrocopy FQSGGNRGRGRGGKRRNQSGKNVMVEPQQHESVFICGGKEHALVAKNLVPGESVYGEKRVSIAEGDDKIE

Parental  YRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINL
          YRAWNPF.SKL.AAILGGVDQIHIK.GAKVLYLGAASGTTVSHVS.IVGPDGLVYAVEFS..SG.DLINL
Retrocopy YRAWNPFSSKLVAAILGGVDQIHIKLGAKVLYLGAASGTTVSHVSNIVGPDGLVYAVEFSRHSGHDLINL

Parental  AKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTA
          AKKRTNIIPVIEDARHPHKY.MLIAMVDVIFADVA.PDQTRIVALN.HT.LRNGGHFVISIKANC..STA
Retrocopy AKKRTNIIPVIEDARHPHKYCMLIAMVDVIFADVALPDQTRIVALNTHTLLRNGGHFVISIKANCMNSTA

Parental  SAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPPKVKN
          SAEAVFASEVKKMQQENMK.QEQLTLEPYERDHAVVVGVYRP..KVKN
Retrocopy SAEAVFASEVKKMQQENMKAQEQLTLEPYERDHAVVVGVYRPHHKVKN

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_3774 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3774 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 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002579	1 retrocopy	retro_btau_108,
Canis familiaris	ENSCAFG00000005412	1 retrocopy	retro_cfam_1697,
Homo sapiens	ENSG00000105202	1 retrocopy	retro_hsap_99,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Microcebus murinus	ENSMICG00000007686	1 retrocopy	retro_mmur_1127,
Mus musculus	ENSMUSG00000046865	4 retrocopies	retro_mmus_1141, retro_mmus_1585, retro_mmus_1609, retro_mmus_89,
Nomascus leucogenys	ENSNLEG00000014234	1 retrocopy	retro_nleu_1947,
Otolemur garnettii	ENSOGAG00000006463	2 retrocopies	retro_ogar_3102, retro_ogar_504,
Pan troglodytes	ENSPTRG00000010982	2 retrocopies	retro_ptro_2208, retro_ptro_3074,
Pteropus vampyrus	ENSPVAG00000010849	1 retrocopy	retro_pvam_231,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sus scrofa	ENSSSCG00000030510	1 retrocopy	retro_sscr_39,
Tupaia belangeri	ENSTBEG00000007755	2 retrocopies	retro_tbel_3774 , retro_tbel_3974,