RetrogeneDB ID: retro_tbel_3055

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_128505:3427..4440(+)
• 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_3055
ATGGATGAGACTGTCGCTGAGTTTATCAGGAGGGCCATCTTGAAAATCCACATGACCGAAATGATGACAATCCTGAACGC
CTGGAACTTTTTGTCTGATAATGAACTGCAGACCATCAGCTTTCTGCAGAGAAAGGAATCTTTGGTTCAGCACTTGATTC
TGCTGTGTGAGGAAAAGCATGCAAGTCTCAATGATGCAGTCCCTTTAGACATCATTTATACTCCAGTTCATCAGCATCAG
AAAGTTTGGGATGTTTTTCAGATGAGTAAAGAACCAGGTGAAGATGTTGATCTTTTTGATCTGGAACAATTCAAAAGTTC
ATTTAAGAAAATTCTTTAGCGAGCACCGAAAAATGTGACGGTCAGCTTCAGAGACACGGAGGAGGACGCAGTCTGGATCC
GAATTGCCTGGGGAACACAGTACAGGAAGCCAAACCAGTACAAACCTACTTAGGTGGTGCATCACTCCTAGACTCCGTAT
GCCTTCATCTCTTTCTTCCGGCTGAGAAGCAATATACCCCTTCTGGGTCAGGCACTGACAACTGCTAGTAAACACCATCA
GATTGTGAAAATGGACCTGCGGAGCCACTATCTGGACTCTCTGAAGGCTATTACTTTTAAACAGTATAACCAGACCTTTG
AAATTCACAACTCTACAACACCTTTAGAGGAACGAAGCCTTGGACTAGATATAAATATAGATTCAAGGATGATTCATAAA
AACACAACAGAAAAAAACAGAGTGCAGAGAGTAACTCAAGAAACTTTTGGAGACTACCCTCAACCATGACTGGAATTTGC
ACAATACAAGCTTGAGATGAAGTTCCAAAGTGACTTAACGGGGGGCGTCTTGAGAGGCAAGAACCCCTCCAGTGTCTGAT
AAAGTTCTTGAGCCCACACCTTTTGGAAGCGTTGAAATCCTTAGCGCCAGCCGGTATTGCAGATACACCACTTTCTCTGT
TGCTCACTTGTATACCCAACAAGGGAATGAATTATTTTAAAATTTGAGATAAA

Alignment

ORF - retro_tbel_3055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.41 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDETVAEFIRRTILKIRMTEMMTILKAWNFLSDNELQTINFRQRKESLVQHLILLCEEKHASLNDAALLD
          MDETVAEFIRR.ILKI.MTEMMTIL.AWNFLSDNELQTI.F.QRKESLVQHLILLCEEKHASLNDA..LD
Retrocopy MDETVAEFIRRAILKIHMTEMMTILNAWNFLSDNELQTISFLQRKESLVQHLILLCEEKHASLNDAVPLD

Parental  IIYTQVHQHQKGWDVFQMSKE-GEDVDLFDMEQFKSSFKKILQRALKNVTVSFRDTEENAVWIRIAWGTQ
          IIYT.VHQHQK.WDVFQMSKE.GEDVDLFD.EQFKSSFKKIL.RA.KNVTVSFRDTEE.AVWIRIAWGTQ
Retrocopy IIYTPVHQHQKVWDVFQMSKEPGEDVDLFDLEQFKSSFKKIL*RAPKNVTVSFRDTEEDAVWIRIAWGTQ

Parental  YTKPNQYKPTYVVHYSQTPYAFISFSRLRSNIPLLGQALTIASKHHQIVKMDLRSHYLDSLKAIVFKQYN
          Y.KPNQYKPT.VVH.S.TPYAFISF.RLRSNIPLLGQALT.ASKHHQIVKMDLRSHYLDSLKAI.FKQYN
Retrocopy YRKPNQYKPT*VVHHS*TPYAFISFFRLRSNIPLLGQALTTASKHHQIVKMDLRSHYLDSLKAITFKQYN

Parental  QTFEIHNSTTPLEERSLGLDINIDSRIIHENAIEKNRVQRVTQETFGDYPQPRLEFAQYKLETKFKSDL-
          QTFEIHNSTTPLEERSLGLDINIDSR.IH.N..EKNRVQRVTQETFGDYPQP.LEFAQYKLE.KF.SDL.
Retrocopy QTFEIHNSTTPLEERSLGLDINIDSRMIHKNTTEKNRVQRVTQETFGDYPQP*LEFAQYKLEMKFQSDL<

Parental  NGGVLAERQEPLRCLIKFSSPHLLEALKSLAPAGIADAPLSPLLTCIPNKGMNYFKIRDK
          NGG.L.ERQEPL.CLIKF.SPHLLEALKSLAPAGIAD.PLS.LLTCIPNKGMNYFKI.DK
Retrocopy NGGRL-ERQEPLQCLIKFLSPHLLEALKSLAPAGIADTPLSLLLTCIPNKGMNYFKI*DK

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_3055 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3055 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 ,