RetrogeneDB ID: retro_tbel_176

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1376:115446..116461(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKAP2
• Ensembl ID: ENSTBEG00000005807
• Aliases: None
• Description: cytoskeleton associated protein 2 [Source:HGNC Symbol;Acc:1990]

Sequence

>retro_tbel_176
AAGCAGTGCAGACACACTGTAGCAAAAGCAACTACTGATAGTGCATCAGCCCAGCCCAAAGACACTGCAGAAGAGAGAGG
CTGGTCTGCTGAATGGAAAGCCGGCAAAGGAAGAATGCTGCGAAGGCCACCTCATTCAGTAGTTGCTCAGCCCGCGTCTG
AAGCACAAAATCAAAAACCAGTTAGGTCCATCTGGACTACCATGGCAGAAGATGAACAAAGATTATTTACTGAAAAAGTG
AATAAGACATTTTCTGAATGCCTGAACCTAATTAATGAGAGATGCCCAAAAGAAGAAATATTGGTCACACTGAATGACTT
GATTAAAAAATATTACAGATGCCAAAACCCTCGTTAAATATTGGATATGTCTTGTCTGTACTGAACCAATCCCAAGTCCT
AGTGAAGATATTATCACAATTTATGAGCAGGCCATTCTGGCAGGGGCTCAGCCCACTGAAGAGATGTGGCATGTGATTGT
AGATATTATCACATGAAGAATCAAGAAAAAGTTATTTTCGAGAAAAATACGGAGGATGATTGCATAACCAAAGAACAAAT
CCAAGAAGTCAACACTGAATATATAGGTGTAAATCTACAGCCAGGAAAACCGGAAATGGAGAATAAACATCCTTGAAATT
GGTATTTGGGGATTGTGAGAAGGAGCAAGATGACAACACAAAAGATTCACCCTGCCATGGTAAAACTCCCAATACAGAAA
CTAGGGCGGGTTGCTTAATGAAATATAATGTGTCTGCTCCATACTTGCAAAGTATAAAGAAGGAGCAATGTGATGAAATA
AATTCTACATTCGAAGAGCTGAAATTTCCGACAGCAGTGAAACAATCTCAACATCTTCCAGAGAAGACTTCTACATTGTC
AGACACGTTAAAAGACCATTATTTTTGTGTGTCTTCATTGGAACAGTTCACAGAGTTAGGAAGTGAAACCGACGCTTCCG
TATGCCGCCCTAGTGCAGCACTGTGCTGGACGCACCCGACACTGAGACAGCAGAA

Alignment

ORF - retro_tbel_176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.49 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EQRRHTIAKVTTDSRSAQPKETAEERKARLSEWKANKGRMVKRPPNSVVTQPEPEAQNQKPVGSFWTTMA
          .Q.RHT.AK.TTDS.SAQPK.TAEER.....EWKA.KGRM..RPP.SVV.QP..EAQNQKPV.S.WTTMA
Retrocopy KQCRHTVAKATTDSASAQPKDTAEER-GWSAEWKAGKGRMLRRPPHSVVAQPASEAQNQKPVRSIWTTMA

Parental  EEDEQRLFTEKVNKTFSECLNLINEGCPKEEVLVTLNDLIK-NIPDAKKLVKYWICLARIESITSSIEDI
          E.DEQRLFTEKVNKTFSECLNLINE.CPKEE.LVTLNDLIK.NI.DAK.LVKYWICL...E.I.S..EDI
Retrocopy E-DEQRLFTEKVNKTFSECLNLINERCPKEEILVTLNDLIK>NITDAKTLVKYWICLVCTEPIPSPSEDI

Parental  IALYEQGILAGAHPIEEMRHVIVDIIT-MKNQEKEKVNLEKNTEDDCVTQEQIQEVDTEYVGVNLQLGKP
          I..YEQ.ILAGA.P.EEM.HVIVDIIT.MKNQ..EKV..EKNTEDDC.T.EQIQEV.TEY.GVNLQ.GKP
Retrocopy ITIYEQAILAGAQPTEEMWHVIVDIIT<MKNQ--EKVIFEKNTEDDCITKEQIQEVNTEYIGVNLQPGKP

Parental  ETENKHHRN-VVFQDCEKEQDDKTKESTCDVKTPNTETRAGCLIKYNVSTTPYLQSEKKKVQFDEINSTF
          E.ENKH..N..VF.DCEKEQDD.TK.S.C..KTPNTETRAGCL.KYNVS..PYLQS.KK..Q.DEINSTF
Retrocopy EMENKHP*N<LVFGDCEKEQDDNTKDSPCHGKTPNTETRAGCLMKYNVS-APYLQSIKKE-QCDEINSTF

Parental  KEVKFLTPVR-SQCLQEKASKLPDMLKDHYLYVSLLKQLMELGSETDAFICCHNAALCQMY-FETETAE
          .E.KF.T.V..SQ.L.EK.S.L.D.LKDHY..VS.L.Q..ELGSETDA..C...AALC......TETAE
Retrocopy EELKFPTAVKQSQHLPEKTSTLSDTLKDHYFCVSSLEQFTELGSETDASVCRPSAALCWTH<PDTETAE

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_176 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_176 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005898	1 retrocopy	retro_cfam_968,
Choloepus hoffmanni	ENSCHOG00000009905	2 retrocopies	retro_chof_1493, retro_chof_973,
Cavia porcellus	ENSCPOG00000012382	1 retrocopy	retro_cpor_171,
Felis catus	ENSFCAG00000010021	1 retrocopy	retro_fcat_1770,
Myotis lucifugus	ENSMLUG00000000132	1 retrocopy	retro_mluc_1515,
Monodelphis domestica	ENSMODG00000010436	1 retrocopy	retro_mdom_1364,
Mustela putorius furo	ENSMPUG00000017996	1 retrocopy	retro_mputfur_1270,
Mus musculus	ENSMUSG00000037725	1 retrocopy	retro_mmus_2651,
Otolemur garnettii	ENSOGAG00000008428	1 retrocopy	retro_ogar_1743,
Tupaia belangeri	ENSTBEG00000005807	1 retrocopy	retro_tbel_176 ,
Tupaia belangeri	ENSTBEG00000013625	2 retrocopies	retro_tbel_1637, retro_tbel_4436,
Tursiops truncatus	ENSTTRG00000009624	2 retrocopies	retro_ttru_1491, retro_ttru_1741,