RetrogeneDB ID: retro_tbel_4700

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_98074:75937..76530(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDKN3
• Ensembl ID: ENSTBEG00000010203
• Aliases: None
• Description: cyclin-dependent kinase inhibitor 3 [Source:HGNC Symbol;Acc:1791]

Sequence

>retro_tbel_4700
GACTCATCAGATGAAGAACCTGTTGAAGAATAAACTCCAATTCAGATGTGGCTACCTGTGTCATAAGTGAACTGTTCTCA
GTTTCTTGATTTATGTGCTCTTCCAGGATGCAAATTTAAAGATATTAAAAGAAATATCCCCAAAATACAGAGGAACTAAA
GAGCTATGGTATACAAGATTTATTTGTTTTCTGCACCATAGAGAAACTGTCAAAATATAGAATTCCAAGCCTCTTGAACC
TCTAGCAGGACTACGGAATTATTATCCATCATCATCCAAACCCAGGTGGAAAGACTCCTGACATAGCCAGATGCTGTGAA
ATAACAGTGGAACTTGTTATCTGCCTTAGAAATAACCAAAAAACTCTAATACACTGTCACAGAGGACTTGAGAGGTCTTG
TCTTGTAGCCCCTTACCTCCTGCTATACCCTTCTGACATAGTACCATCACAGAAAGCCATAGACACCCTGTGAGACCTAA
AAGGATCTGGTGTCATACAGAGCACAAAGCAACATAAATATCTTCATGAGTTCCAGGACAAACTAGCTGCACACCTGTCT
TCAAGAGAGTCACTATTAAGATCTGTATCAAGA

Alignment

ORF - retro_tbel_4700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.14 %
• Parental protein coverage: 94.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSSDEEPIEDEQTPIQISWLPLSQVNCSQFLGLCALPGCKFKDVRRNIQK-DTEELKNYGIQDIFFFCT-
          DSSDEEP.E.E.TPIQ..WLP.S.VNCSQFL.LCALPGCKFKD..RNI.K..TEELK.YGIQD.F.FCT.
Retrocopy DSSDEEPVE-E*TPIQM-WLPVS*VNCSQFLDLCALPGCKFKDIKRNIPK<NTEELKSYGIQDLFVFCTI

Parental  RGLSKYRVPNLLNFYQQYGIITHHHPIPDGGTPDIASCCEIMEELAICVKNNRKTLIQCYGELGRSCLVA
          ..LSKYR.P.LLN..Q.YGII.HHHP.P.G.TPDIA.CCEI..EL.IC..NN.KTLI.C...L.RSCLVA
Retrocopy EKLSKYRIPSLLNL*QDYGIIIHHHPNPGGKTPDIARCCEITVELVICLRNNQKTLIHCHRGLERSCLVA

Parental  ACLLLYLSDTVSPQQAIDSMRDLRGSGAIQTIKQYNYLHEFRDKLAAHLSSRDSLLRSVSR
          ..LLLY.SD.V..Q.AID...DL.GSG.IQ..KQ..YLHEF.DKLAAHLSSR.SLLRSVSR
Retrocopy PYLLLYPSDIVPSQKAIDTL*DLKGSGVIQSTKQHKYLHEFQDKLAAHLSSRESLLRSVSR

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_4700 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4700 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012823	1 retrocopy	retro_chof_1806,
Echinops telfairi	ENSETEG00000018617	1 retrocopy	retro_etel_1763,
Felis catus	ENSFCAG00000015089	2 retrocopies	retro_fcat_135, retro_fcat_626,
Loxodonta africana	ENSLAFG00000014833	1 retrocopy	retro_lafr_637,
Macropus eugenii	ENSMEUG00000002497	3 retrocopies	retro_meug_1255, retro_meug_1768, retro_meug_1849,
Procavia capensis	ENSPCAG00000015559	1 retrocopy	retro_pcap_104,
Sarcophilus harrisii	ENSSHAG00000008977	1 retrocopy	retro_shar_502,
Tupaia belangeri	ENSTBEG00000010203	2 retrocopies	retro_tbel_1809, retro_tbel_4700 ,