RetrogeneDB ID: retro_tbel_2255

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_107315:3553..4224(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRIM1
• Ensembl ID: ENSTBEG00000012998
• Aliases: None
• Description: primase, DNA, polypeptide 1 (49kDa) [Source:HGNC Symbol;Acc:9369]

Sequence

>retro_tbel_2255
GGCAGTCAAGATGTTAAAAAGAAAGTTCACCTAAGTGAAAAATTTCACCCTTTTGTCAGAAAATCTATAAACATGATGTA
AATATACTTTGAGGAATATGTTTCAGTTGATCAAGATATTCTTAAAAATAAAGAATGCAGGGATAAGATCTTAGCCCTTG
TTCCTGAAATAAATTATGATGAACTTCAACAAAACTTCCAAGTCTTCACAGTTCACTTCAGCATTGGAAGCAGTTGAAAA
AAGTACCCAGCAGATATCAGAATAACATAGAAAATGACAAATGTAGATCCTGGCTGGAGTGGCAGATCATACTCCAGTAC
TATTTCCTATGGCTGGATGTCAATGTTCGCAAAGGAATCAGTCATTTACTGAAGAGCCATTTTAGTGTTTATCCTGAAAA
AGGTCATATCTCTGTGACTATCAGTTTACAAGAAATGGATCAGTTTAATCCATTTAGCATTCCAATCACAAGCTCCCTCC
TGTCATGAGTTGGATGCCATTTCCAATAATGAAGAGGAAAAAGAGAATGATGCTGAATCTGAAATCCAACATAGAACTAG
AGATTGTAAGAGGATCAGTCTAGCACGTTATATGAAAGTTGTTTTTAACATTTTCTTGAAAACGTGGATAAATCCCAAAA
AGGTGTACTTCTCAAGAAGAGTGATGTACAA

Alignment

ORF - retro_tbel_2255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.1 %
• Parental protein coverage: 53.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGQDVKKKVHLSEKIHPFVRKSINIIKKYFEEYALIGQDILENKESWDKILALIFLNDPSPNHDELQQNF
          G.QDVKKKVHLSEK.HPFVRKSIN....YFEEY....QDIL.NKE..DKILAL.....P..N.DELQQNF
Retrocopy GSQDVKKKVHLSEKFHPFVRKSINMM*IYFEEYVSVDQDILKNKECRDKILALV----PEINYDELQQNF

Parental  Q-KSHNSLQRWEHLKKVASKYQNNIKNDKCGPWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTG
          Q...H.SLQ.W..LKKV.S.YQNNI.NDKC..WLEW.I.LQY.F..LD.NV.KGI.HLLKS.FSV.P..G
Retrocopy Q<SLHSSLQHWKQLKKVPSRYQNNIENDKCRSWLEWQIILQYYFLWLDVNVRKGISHLLKSHFSVYPEKG

Parental  RISVPIDLQKVDQFDPFSVPTISSI-CHELDAISTNEEEKEENDGESDIKHRTRDYKKTSLAPYVK-VFE
          .ISV.I.LQ..DQF.PFS.P..SS..CHELDAIS.NEEEK.END.ES.I.HRTRD.K..SLA.Y.K.VF.
Retrocopy HISVTISLQEMDQFNPFSIPITSSL>CHELDAISNNEEEK-ENDAESEIQHRTRDCKRISLARYMKVVFN

Parental  HF-LENLDKSRKGELLKKSDLQ
          .F.LEN.DKS.KG.LLKKSD.Q
Retrocopy IF<LENVDKSQKGVLLKKSDVQ

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_2255 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2255 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255 ,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,