RetrogeneDB ID: retro_tbel_534

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2362:152558..153172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA3
• Ensembl ID: ENSTBEG00000001905
• Aliases: None
• Description: cell division cycle associated 3 [Source:HGNC Symbol;Acc:14624]

Sequence

>retro_tbel_534
CAGCAGGAAAACAGCAGGACATAGACCCCCACTCTCCCACCCTCGGCATTGCAGATACCTATGAAGACCAGCAGCAGAGA
CCCTTCAAGCTCACTGGTGACACACCTGAGTAAACTATTTGACAGTTGAGATTGAAGTCTCCAATCGAATCTCCCCACAG
AGCCTGTTCTGCCCTGGGAACACTTTTACCTTTTGAATTGGACTTGCCTCTGGTACCCAGTCATCTTTTGAGGACCAAAT
GCTACCTTAGAACTAAACCGAGTTCCCCTGCAAACAGGCCTTTTCCAAGGAGGAAGCGAGACAGCCCCCGGAAACTCCTG
TGGCCAGCCAGAGTGGAGAGGAGCCCTCGAGAAACCCCGAGACTCCCCGACATTCAGGTTGTAAGCACAATAGATAGAAA
CCAAGTAGCAAGGTCCTAGGGAGATCCTCTCTCACCATCCTGCAGGATGACAACTCCTCCAGGACCCTGACATCATGTCA
GGGTAAAGCGGCCTTCTTCCCTAACTGAAAATGTTAGAAAACTAGAGGAAGGAGCCATTCTTGGGACCGTACGGCTTCTA
AAAACTGCAGGACAAGCCCCGGAACAAGGCCAGGACCATGACAAGGAGAACCAG

Alignment

ORF - retro_tbel_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.94 %
• Parental protein coverage: 75.28 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QAQDTDPRSPTL--GIARTPMKTSSGDPPSPLVKQLSDVFET-EVSTSSLPP-EPVLPLEE-PLPSELDL
          Q........PTL.......PMKTSS.DP.S.LV..LS..F.....S..S..P.EPVLP.E...LP.ELDL
Retrocopy QQENSRT*TPTLPPSALQIPMKTSSRDPSSSLVTHLSKLFDS*D*SLQSNLPTEPVLPWEH<LLPFELDL

Parental  PL-GTQLFLEDQMPSWNQTELPCKQAFSKEEARQSPKTPVASQSGDKPLRDPETPRSSGSKCSRRKPNSK
          PL.GTQ...EDQM...N.TE.PCKQAFSKEEARQ.P.TPVASQSG..P.R.PETPR.SG.K..R.KP.SK
Retrocopy PL<GTQSSFEDQMLP*N*TEFPCKQAFSKEEARQPPETPVASQSGEEPSRNPETPRHSGCKHNR*KPSSK

Parental  VLGRSPLTILQDDNSPGTLTSRQG-KRPCPLSENVRELKEGAIPGTGRLLKPGGRALEQGQGHDKENQ
          VLGRS.LTILQDDNS..TLTS.QG.KRP..L.ENVR.L.EGAI.GT.RLLK..G.A.EQGQ.HDKENQ
Retrocopy VLGRSSLTILQDDNSSRTLTSCQG>KRPSSLTENVRKLEEGAILGTVRLLKTAGQAPEQGQDHDKENQ

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_534 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_534 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013985	1 retrocopy	retro_amel_1158,
Canis familiaris	ENSCAFG00000014650	4 retrocopies	retro_cfam_1100, retro_cfam_1940, retro_cfam_345, retro_cfam_633,
Cavia porcellus	ENSCPOG00000012334	1 retrocopy	retro_cpor_1073,
Felis catus	ENSFCAG00000004274	2 retrocopies	retro_fcat_1182, retro_fcat_1942,
Mustela putorius furo	ENSMPUG00000016781	1 retrocopy	retro_mputfur_663,
Pteropus vampyrus	ENSPVAG00000012300	4 retrocopies	retro_pvam_235, retro_pvam_248, retro_pvam_297, retro_pvam_667,
Rattus norvegicus	ENSRNOG00000015529	1 retrocopy	retro_rnor_2685,
Ictidomys tridecemlineatus	ENSSTOG00000023573	1 retrocopy	retro_itri_804,
Tupaia belangeri	ENSTBEG00000001905	1 retrocopy	retro_tbel_534 ,
Vicugna pacos	ENSVPAG00000009784	1 retrocopy	retro_vpac_296,