RetrogeneDB ID: retro_tbel_587

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2491:80018..80783(-)
• Located in intron of: ENSTBEG00000012585

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK7
• Ensembl ID: ENSTBEG00000012193
• Aliases: None
• Description: cyclin-dependent kinase 7 [Source:HGNC Symbol;Acc:1778]

Sequence

>retro_tbel_587
CATATATCTGAAGCAAAAGATGATATAAATAGAACAGTCTTAAGAAAGATGAGATTACTACAGGAGCTAAGTCATCCAAA
TATAATTGTTCTCCTTGATGCTTTTGGACATAAATCTAATATTAGCCTTGTCTTTGATTTTATGGACACGAACTAGAGGC
ATAATAAGGGATAATAGCCTTATGCTGACACCATCACACATCAAAGCCTGCATGCCGATGACTCTTCAAGGGTTACATCA
ACAGTAGATTCTACATAGGGATTTGAAACCAAACAACTGGTTGCTTGATGAAAATGGAGTTCTAAAACTGGTAGATTTTG
GCCTGGTCAAATCACTCAGAAGCCCTGATAGAGCTTATATGCATCAGGTTGTAACCAGGTGGTATCAGGCCCCTGAGTTA
CTATCTGGAGCTAGGAGTATGGTGTGGATGTAGACATGTGGGCGGTTGGCTATATACTAGCAGATTTGTTTCTGGAGGTT
CCTTTTTTGCCAGAAGATTCAGACATCAATCAATTAACAAAAATTTTTGAAACTTTGGGCACACCAACTGAGGAATAGTG
GCCTGCCATGTGTAGTAATCTTCCAGATTATGTGACATTTAAGAGTTTTCCTGGAATCCCATTGCAACATAACTTCATTG
CAGCTGGAGATGACTTGCTAGATCTCATACAAGGTTTATGCTTATTTAATCTATGCACTCGAATTATGGCCACACAGGCA
TTAAAAACTAAGTATTTCAGTAACTGGCCAGGGCCAACATCTGGA

Alignment

ORF - retro_tbel_587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.53 %
• Parental protein coverage: 97.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMET-DLEV-IIKDNSLVLTPSHV
          H.SEAKD.INRT.LR...LLQELSHPNII.LLDAFGHKSNISLVFDFM.T..LE..II.DNSL.LTPSH.
Retrocopy HISEAKDDINRTVLRKMRLLQELSHPNIIVLLDAFGHKSNISLVFDFMDT<ELEA<IIRDNSLMLTPSHI

Parental  KAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELL
          KA.M.MTLQG...LHQ..ILHRDLKPNN.LLDENGVLKL.DFGL.KS..SP.RAY.HQVVTRWY.APELL
Retrocopy KACMPMTLQG---LHQQ*ILHRDLKPNNWLLDENGVLKLVDFGLVKSLRSPDRAYMHQVVTRWYQAPELL

Parental  FGARM-YGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCS-LPDYVTFKSF
          .GAR..YGV.VDMWAVG.ILA.L.L.VPFLP.DSD..QLT.IFETLGTPTEE.WP.MCS.LPDYVTFKSF
Retrocopy SGARS<YGVDVDMWAVGYILADLFLEVPFLPEDSDINQLTKIFETLGTPTEE*WPAMCSNLPDYVTFKSF

Parental  PGIPLQHIFIAAGDDLLDLIQGLFLFNPCTRITATQALKTKYFSNRPGPTPG
          PGIPLQH.FIAAGDDLLDLIQGL.LFN.CTRI.ATQALKTKYFSN.PGPT.G
Retrocopy PGIPLQHNFIAAGDDLLDLIQGLCLFNLCTRIMATQALKTKYFSNWPGPTSG

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_587 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_587 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000134058	1 retrocopy	retro_hsap_2335,
Gorilla gorilla	ENSGGOG00000013349	1 retrocopy	retro_ggor_1772,
Mus musculus	ENSMUSG00000069089	1 retrocopy	retro_mmus_383,
Otolemur garnettii	ENSOGAG00000010748	1 retrocopy	retro_ogar_986,
Procavia capensis	ENSPCAG00000002566	1 retrocopy	retro_pcap_318,
Pongo abelii	ENSPPYG00000015525	1 retrocopy	retro_pabe_2114,
Pan troglodytes	ENSPTRG00000016946	1 retrocopy	retro_ptro_1707,
Tupaia belangeri	ENSTBEG00000012193	2 retrocopies	retro_tbel_587 , retro_tbel_637,