RetrogeneDB ID: retro_tsyr_1402

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_42780:4900..5758(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB2
• Ensembl ID: ENSTSYG00000013818
• Aliases: None
• Description: cyclin B2 [Source:HGNC Symbol;Acc:1580]

Sequence

>retro_tsyr_1402
GATGCCTTGCTCTGCGAGATCAAGGATGTTGATAACGAAGAGTTGGAGAACCCTCAAATCTACAGTGACTAGAAGGCTAT
CTACTGGTACCTCAGGCAGCTGGAAGTTTTGCAACTCATTAACCCATGTTTCTTAGATGGAAGAGATATAGATGGATGTA
TTCATGCCATTCTGGTGGATTGGCTGGTGCAAATTCACTGCAAGTTCAGGCTTCTGCTAGAGACTCTGTATATGTGCGTT
GCCATGCTGGATCAGTTTTTACAGGCTCAGCCATTTTCCCATAAGAATCTTCAACTGGTGATTACTGCTCTGCTCTTGAC
TTCCAAGTAGGAAGAGATGTTTTCTCCAAATATTGGAGACTTCGTTGACATCACAGAGAATGCTTATACCAGTTCCCAAA
CTTAAGAAATGGAAATTTCAATTTTGAAAGAACTGAAATTTGAGTTGGATCAACTCTTGCAACTGTATTTCCTAAAGTAG
ACATCAAAAGCCAGGGAGGTTGATGTTGAAAAGCACACTGTGGCCAAATATTTGATGGAGCTGATCCTCATTGACTATGA
CATGGTCATTTTATCACCCTTCTAAGGTAGCTGCAGCTGCTTCCTGCTTGTCTCAGACGGTTTTAGGCCAAGGAAAATGG
AACTTAAAGCAGCAGTATTACACAGGATACACAAAGGATGAAGTATTGGATGTGATGCAGCACATGGCCAAAAGCGTGGC
GAAAGTCAAGAAAACTTAACCAAGTTGATTGCCCTCAAAAATAAGTATGCAAACAGCAAACTCCTGAAGATCAGCACTAT
CCTCCAGCTGAATTTCAAAGCCATCAAAGACTTGGCCTCCCCTCTCATGGGAAGATCT

Alignment

ORF - retro_tsyr_1402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.62 %
• Parental protein coverage: 72.36 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DALLCKIEDIDNEDSENPQLCSDYVKDIYQYLRQLEVSQSINPHFLDGRDINGRMRAILVDWLVQVHSKF
          DALLC.I.D.DNE..ENPQ..SD..K.IY.YLRQLEV.Q.INP.FLDGRDI.G...AILVDWLVQ.H.KF
Retrocopy DALLCEIKDVDNEELENPQIYSD*-KAIYWYLRQLEVLQLINPCFLDGRDIDGCIHAILVDWLVQIHCKF

Parental  RLLQETLYMCVAIMDRFLQAQPVSRKKLQLVGITALLLASKYEEMFSPNIEDFVYITDNAYTSSQIREME
          RLL.ETLYMCVA..D.FLQAQP.S.K.LQLV.ITALLL.SK.EEMFSPNI.DFV.IT.NAYTSSQ..EME
Retrocopy RLLLETLYMCVAMLDQFLQAQPFSHKNLQLV-ITALLLTSK*EEMFSPNIGDFVDITENAYTSSQT*EME

Parental  TSILKELKFELGRPLPLHFLRRASKAGEVDVEQHTLAKYLMELTLIDYDMV-HYHPSMVAAAASCLSQKV
          .SILKELKFEL...L.L.FL...SKA.EVDVE.HT.AKYLMEL.LIDYDMV..YHPS.VAAAASCLSQ.V
Retrocopy ISILKELKFELDQLLQLYFLK*TSKAREVDVEKHTVAKYLMELILIDYDMV>FYHPSKVAAAASCLSQTV

Parental  LGQGKWNLKQQYYTGYTEDEVLDVMQHMAKNVVKV-NENLTKFIAIKNKYASSKLLKISTIPQLNSKAIK
          LGQGKWNLKQQYYTGYT.DEVLDVMQHMAK.V.KV..ENLTK.IA.KNKYA.SKLLKISTI.QLN.KAIK
Retrocopy LGQGKWNLKQQYYTGYTKDEVLDVMQHMAKSVAKV<QENLTKLIALKNKYANSKLLKISTILQLNFKAIK

Parental  DLASPLMGRS
          DLASPLMGRS
Retrocopy DLASPLMGRS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1402 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005269	1 retrocopy	retro_btau_1584,
Homo sapiens	ENSG00000157456	1 retrocopy	retro_hsap_3816,
Nomascus leucogenys	ENSNLEG00000011543	1 retrocopy	retro_nleu_212,
Otolemur garnettii	ENSOGAG00000012885	2 retrocopies	retro_ogar_1770, retro_ogar_2766,
Pongo abelii	ENSPPYG00000006517	2 retrocopies	retro_pabe_3073, retro_pabe_3074,
Pan troglodytes	ENSPTRG00000007123	1 retrocopy	retro_ptro_2597,
Ictidomys tridecemlineatus	ENSSTOG00000001275	1 retrocopy	retro_itri_229,
Tarsius syrichta	ENSTSYG00000008928	1 retrocopy	retro_tsyr_232,
Tarsius syrichta	ENSTSYG00000013818	1 retrocopy	retro_tsyr_1402 ,