RetrogeneDB ID: retro_tbel_4151

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_68923:4479..5095(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK2
• Ensembl ID: ENSTBEG00000005123
• Aliases: None
• Description: cyclin-dependent kinase 2 [Source:HGNC Symbol;Acc:1771]

Sequence

>retro_tbel_4151
ATAGAAGACTATACAAAAATAGAGGAAATTGGAGAAGGTACCTATGGAGTTGTGTATTAGGGCAGACACAAAACTACAGG
TCAAGTGGTAGCTATGAAGAAAATAAGACTAGAAAGTGAAGAGGAAGGGGTTCCTAGTACTGTGATTTGGGAAGCTCTCT
ATTAAAAGAACTTCATCATCCAAATATAGTCAGTCTTCAAGATGTGCTCATGCAGGATTCCAGGTTGTATCTCATCTTTG
AATTTCTTTCCATGGATCTCAAGAAATACTTGGGTTCTATACTTCCTGGTCAGTTCATGGACTCCTCACTTGTTAAGAAT
TATTTGTACCAAATCCTACAAGGGATTGTGTTTTGTCACTCTAGAAGAGTTCTTCATAGAGACTTAAGACCTCAAAGCCT
ATTAATCAATGGCAAAGGAACAATTACACTGGCTGATTTTGGCCTTGCCAGAGCTTTTGGAATACCAATTAGAGTATACA
TCCATGAGGTGGTGACGCTCCGGTACAGATCTCCAGGGTATGGCTGGGGTCAGCCTGTTACTCAACTCCGATTGACATTT
GGAATATTGGGGCCATATTTACAGAATTAGCCACCAAGAAACCACTTTTCTATGGG

Alignment

ORF - retro_tbel_4151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.29 %
• Parental protein coverage: 84.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MENFQEVEKIGEGTYGVVYKAKNKLTGEVVALKKIRLDTETEGVPSTAIREI-SLLKELNHPNIVKLLDV
          .E.....E.IGEGTYGVVY....K.TG.VVA.KKIRL..E.EGVPST.I.E..SLLKEL.HPNIV.L.DV
Retrocopy IEDYTKIEEIGEGTYGVVY*GRHKTTGQVVAMKKIRLESEEEGVPSTVIWEA<SLLKELHHPNIVSLQDV

Parental  IHTENKLYLVFEFLHQDLKKFMDASALTG--IPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINT
          ......LYL.FEFL..DLKK....S.L.G......L.K.YL.Q.LQG..FCHS.RVLHRDL.PQ.LLIN.
Retrocopy LMQDSRLYLIFEFLSMDLKKYL-GSILPGQFMDSSLVKNYLYQILQGIVFCHSRRVLHRDLRPQSLLING

Parental  EGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAP-EILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPG
          .G.I.LADFGLARAFG.P.R.Y.HEVVTL.YR.P....LG...YST..DIW..G.IF.E..T...LF.G
Retrocopy KGTITLADFGLARAFGIPIRVYIHEVVTLRYRSP<RVWLGSACYSTPIDIWNIGAIFTELATKKPLFYG

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_4151 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4151 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003168	1 retrocopy	retro_amel_1525,
Bos taurus	ENSBTAG00000004021	1 retrocopy	retro_btau_1424,
Erinaceus europaeus	ENSEEUG00000014081	1 retrocopy	retro_eeur_445,
Pteropus vampyrus	ENSPVAG00000007555	1 retrocopy	retro_pvam_794,
Tupaia belangeri	ENSTBEG00000005123	1 retrocopy	retro_tbel_4151 ,
Tupaia belangeri	ENSTBEG00000017549	3 retrocopies	retro_tbel_3309, retro_tbel_807, retro_tbel_812,