RetrogeneDB ID: retro_tbel_2049

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_837:1066168..1066759(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPN
• Ensembl ID: ENSTBEG00000000039
• Aliases: None
• Description: centromere protein N [Source:HGNC Symbol;Acc:30873]

Sequence

>retro_tbel_2049
AAGACTATTGCTGAGTTTATCAGGAGGACCATCTTGAAAATCCACATGACCGAAATGACGACAATCCTAAAAGCCTGGAA
CTTTTTGCCTGAGAATGAACTGCAGACCATAAACTTTAGGCAGAGAAAGGAATCTTTGGTTCGGCACTTGATTCTGCTGT
GTGAGGAAAAGCACGCGAGTCTCAATGATGCAGCCCTTTTAGACATCATTTATATTCAAGTTCATCAGCATCAGAAAGTT
TGGGATGTTTTTCAGATGAGTAAAGAACCAGGTGAAGATGTTGACCTTTTTGATATGGAACATTTCAAAGGTTCGTTTAA
GAAAATTCTTCAGCGAGCACTGAAAAATGTGCTGGTCAGCTTCAGAGACACGGAGGAGAAGGCAGTCTGGATCCGAATTG
CCTGGGGAACACAGTCTAGGAAGCCAAATCGGTACAAACCGACTTACATGGTGTATTACTCCCAGACTCTGTATGCTTTT
GCTTCTTCCTCCCGGCTGAGGAGCCATATACCCCTTCTGAGTCAGGCACTGATAACTGCTGGGAAACACCGTCGGATTGT
GAAAATGGACCTGAGCCACTATCTGGACTCT

Alignment

ORF - retro_tbel_2049 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 58.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETVAEFIRRTILKIRMTEMMTILKAWNFLSDNELQTINFRQRKESLVQHLILLCEEKHASLNDAALLDII
          .T.AEFIRRTILKI.MTEM.TILKAWNFL..NELQTINFRQRKESLV.HLILLCEEKHASLNDAALLDII
Retrocopy KTIAEFIRRTILKIHMTEMTTILKAWNFLPENELQTINFRQRKESLVRHLILLCEEKHASLNDAALLDII

Parental  YTQVHQHQKGWDVFQMSKE-GEDVDLFDMEQFKSSFKKILQRALKNVTVSFRDTEENAVWIRIAWGTQYT
          Y.QVHQHQK.WDVFQMSKE.GEDVDLFDME.FK.SFKKILQRALKNV.VSFRDTEE.AVWIRIAWGTQ..
Retrocopy YIQVHQHQKVWDVFQMSKEPGEDVDLFDMEHFKGSFKKILQRALKNVLVSFRDTEEKAVWIRIAWGTQSR

Parental  KPNQYKPTYVVHYSQTPYAFISFSRLRSNIPLLGQALTIASKHHQIVKMDLRSHYLDS
          KPN.YKPTY.V.YSQT.YAF.S.SRLRS.IPLL.QAL..A.KH..IVKMDL.SHYLDS
Retrocopy KPNRYKPTYMVYYSQTLYAFASSSRLRSHIPLLSQALITAGKHRRIVKMDL-SHYLDS

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_2049 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2049 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011635	1 retrocopy	retro_btau_1101,
Felis catus	ENSFCAG00000004978	1 retrocopy	retro_fcat_1852,
Homo sapiens	ENSG00000166451	2 retrocopies	retro_hsap_2146, retro_hsap_2291,
Oryctolagus cuniculus	ENSOCUG00000000024	3 retrocopies	retro_ocun_1676, retro_ocun_1806, retro_ocun_528,
Sarcophilus harrisii	ENSSHAG00000002111	1 retrocopy	retro_shar_331,
Ictidomys tridecemlineatus	ENSSTOG00000007345	1 retrocopy	retro_itri_1431,
Tupaia belangeri	ENSTBEG00000000039	2 retrocopies	retro_tbel_2049 , retro_tbel_3055,