RetrogeneDB ID: retro_tbel_2491

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_111981:7520..8642(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSTBEG00000001289
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein K [Source:HGNC Symbol;Acc:5044]

Sequence

>retro_tbel_2491
AGTATCAGTGCTGATATTGAAACAATTGGACCATATTCGGAAGAAAATCATCCCTTCCTTGGAAGAGGGCCTGCAGTTGC
CATCACCCACTGCAACCAGCCAGCTCCCACTCGAATCTGATGCTGTGGAATGCTTAAATTACCAACACTATAAAGGAAGC
GACTTTGACTGCGAGTTGAGACTGTTGATTCATCAGAGTTTGGCAGGAGGAATTATTGGGGTCAAAGGTGCTAAAATCAA
AGGACTTCAAGAGAACACTCAGACAACAATCAAGCTTTTCCAGGAATGCTGTTCTCATTCCACTGACAGAGTCTTTCTTA
TTGGAGGAAAGCCTGATAGAGTTGTAGAGTGTATAACGATCATCCTTGATCTTATATCTGAGTCTCCTATCAAAGGACGT
GCACAGCTTTATGATCCCAATTTTTACGATGAAACCTATGATTATGGTGGTTTTACCATGATGTTTGATGACCGCTATGG
ACGTCCTGTGGGATTTCCCATGCGGGGAGAGTTGATTTTGACAGAATGCCTCCTGGTCGGGGTGGACGTTCCATGCCTCC
ATCTAGAAGAGATTTTGATGATATGAGCCGTCTTCGAGTACCTCCTCCTCCTGGATGAGGGGGTCAGGGCAGTAGCAGAG
CTCGGAATCTTCCTCTCCCTCCACCACCAGCACCTAGAGGAGGAGATTTAATGGTTTATGACAGAAGAGGAAGACCTGGG
GACCGTTATGATGGCATGGTTGGCTTCAGTGCTGATGAAACTTGGGATTCTGCAATAGATACATGGAGCCCATCTGAATG
GCAGATGGCTTATGAACCTCAGGGTGGCTCTGGATATGATTATTCCTATGCAGGGGGTCGTGGATCATATGGTGATCCTG
GTGGACCTATTATTACTACACAAGTAACTATTCCCAAAGAGTTGGCTGGTTCTATTATTGGCAAAGGAGGTCAGCGAATT
AAACAAATTCGTCATGAATCAGGAGCTTCAATCAAAATTGATGAGCCTTTAGAAGGCTCCAAAGATCGGATCATTACCAT
TACAGGAACACAGGACCAGATACAGAATGCACAGTATTTGCTGCAGAACAGTGTGAAGCAGTATGCAGATATTGAAGGAT
TC

Alignment

ORF - retro_tbel_2491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.68 %
• Parental protein coverage: 81.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SISADIETIG-EILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKGSDFDCELRLLIHQSLAG
          SISADIETIG..I.KKIIP.LEEGLQLPSPTATSQLPLESDAVECLNYQHYKGSDFDCELRLLIHQSLAG
Retrocopy SISADIETIG>HIRKKIIPSLEEGLQLPSPTATSQLPLESDAVECLNYQHYKGSDFDCELRLLIHQSLAG

Parental  GIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISESPIKGRAQPYDP
          GIIGVKGAKIK.L.ENTQTTIKLFQECC.HSTDRV.LIGGKPDRVVECI.IILDLISESPIKGRAQ.YDP
Retrocopy GIIGVKGAKIKGLQENTQTTIKLFQECCSHSTDRVFLIGGKPDRVVECITIILDLISESPIKGRAQLYDP

Parental  NFYDETYDYGGFTMMFDDRRGRPVGFPMRG-RGGFDRMPPGRGGRPMPPSRRDYDDMSPRRGPPPPPPGR
          NFYDETYDYGGFTMMFDDR.GRPVGFPMRG.R..FDRMPPGRGGR.MPPSRRD.DDMS..R...PPPPG.
Retrocopy NFYDETYDYGGFTMMFDDRYGRPVGFPMRG<RVDFDRMPPGRGGRSMPPSRRDFDDMSRLR--VPPPPG*

Parental  GGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAIDTWSPSEWQMAYEPQXX
          GG.G.SRARNLPLPPPP.PRGGDLM.YDRRGRPGDRYDGMVGFSADETWDSAIDTWSPSEWQMAYEPQ..
Retrocopy GGQGSSRARNLPLPPPPAPRGGDLMVYDRRGRPGDRYDGMVGFSADETWDSAIDTWSPSEWQMAYEPQGG

Parental  XXXXYSYAGGRGSYGDPGGPIITTQVTIPKDLAGSIIGKKGQRIKQIHHQSGASIKIDEPLEGSEDRIIT
          ....YSYAGGRGSYGDPGGPIITTQVTIPK.LAGSIIGK.GQRIKQI.H.SGASIKIDEPLEGS.DRIIT
Retrocopy SGYDYSYAGGRGSYGDPGGPIITTQVTIPKELAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSKDRIIT

Parental  ITGTQDQIQNAQYLLHNSVKQYADVEGF
          ITGTQDQIQNAQYLL.NSVKQYAD.EGF
Retrocopy ITGTQDQIQNAQYLLQNSVKQYADIEGF

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_2491 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2491 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468, retro_btau_605,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Microcebus murinus	ENSMICG00000015780	3 retrocopies	retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus	ENSMLUG00000005871	2 retrocopies	retro_mluc_128, retro_mluc_561,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Tupaia belangeri	ENSTBEG00000001289	1 retrocopy	retro_tbel_2491 ,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,