RetrogeneDB ID: retro_tbel_852

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3159:346770..347464(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUV39H2
• Ensembl ID: ENSTBEG00000006477
• Aliases: None
• Description: suppressor of variegation 3-9 homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:17287]

Sequence

>retro_tbel_852
ATCAGCTTAGTAAATGAAGCTACCTTTGGTTGTTCTTGCACAGATTGCTTCTTTGAGAAATGTTGTCCTGTCAAAGTTGG
AGTTCTTTTGGCTTATAGTAAAAAATCAACAAATTAAAATTCCACCTGGAACCCCCATCTATGAATGCAGCTCAAGGTGT
CAATGTGGACCTGATTGTCCCAATAGGATTGTACAACAAGGCACACAGTGTTCACTCTGCATCCTTTGAACTAGCAATGG
CTGTGGCTGGGGTGTAAAAACCCTTGTAAGATTAAAAGAATGAGTTTTGTCATGGAATATGCTGGAGAGGTAATCACAAG
TGAAGAAGCTGAAAGAAGGGGGGCAGTAATAGGACAATAAGGGAATCACGTATCTCTTTGATCTGGACTATGAATCTGAT
GAATTCACAGTGGATGGAGCTCAATATGGAAATGTGTCTTATTTTGTGAATTATAATTGTGACCCAAATCCTCAGGTGTT
CAATATTTTCATTGATAACCTTGATACTCATCTTCCCTGGATAGTATTATTTTCTACAAGAATCATAAATGCTGGAGAAG
AGCTGACTTTTGAATATCAAATGAAAGGTTCTGGAGATATATCTCCAGGTATATCTATTGCCCATAGCCCAGCCAAAAAG
AGGGTGAGAACTGTATGCAAATGTGGAGCTGTAACTTGCAGAGGTTACCTCAAC

Alignment

ORF - retro_tbel_852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.32 %
• Parental protein coverage: 56.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ISLVNEATFGCSCTDCFFEKCCPAEAGVLLAYNK-NQQIKIPPGTPIYECNSRCQCGPDCPNRIVQKGTQ
          ISLVNEATFGCSCTDCFFEKCCP...GVLLAY.K.NQQIKIPPGTPIYEC.SRCQCGPDCPNRIVQ.GTQ
Retrocopy ISLVNEATFGCSCTDCFFEKCCPVKVGVLLAYSK>NQQIKIPPGTPIYECSSRCQCGPDCPNRIVQQGTQ

Parental  YSLCIFRTSNGCGWGVKTLV-KIKRMSFVMEYVGEVITSEEAERRGQLY-DNKGITYLFDLDYESDEFTV
          .SLCI..TSNGCGWGVKTLV.KIKRMSFVMEY.GEVITSEEAERRG....DNKGITYLFDLDYESDEFTV
Retrocopy CSLCIL*TSNGCGWGVKTLV<KIKRMSFVMEYAGEVITSEEAERRGAVI>DNKGITYLFDLDYESDEFTV

Parental  DAARYGNVSHFVNHSCDPNLQVFNVFIDNLDTRLPRIALFSTRTINAGEELTFDYQMKGSGDISSD-SID
          D.A.YGNVS.FVN..CDPN.QVFN.FIDNLDT.LP.I.LFSTR.INAGEELTF.YQMKGSGDIS...SI.
Retrocopy DGAQYGNVSYFVNYNCDPNPQVFNIFIDNLDTHLPWIVLFSTRIINAGEELTFEYQMKGSGDISPGISIA

Parental  HSPAKKRVRTVCKCGAVTCRGYLN
          HSPAKKRVRTVCKCGAVTCRGYLN
Retrocopy HSPAKKRVRTVCKCGAVTCRGYLN

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_852 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_852 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004696	1 retrocopy	retro_cfam_574,
Cavia porcellus	ENSCPOG00000008492	1 retrocopy	retro_cpor_1546,
Homo sapiens	ENSG00000152455	1 retrocopy	retro_hsap_3482,
Gorilla gorilla	ENSGGOG00000028243	1 retrocopy	retro_ggor_2348,
Microcebus murinus	ENSMICG00000002803	1 retrocopy	retro_mmur_340,
Nomascus leucogenys	ENSNLEG00000012108	1 retrocopy	retro_nleu_2202,
Oryctolagus cuniculus	ENSOCUG00000015090	1 retrocopy	retro_ocun_1408,
Ochotona princeps	ENSOPRG00000009465	1 retrocopy	retro_opri_1005,
Pongo abelii	ENSPPYG00000002106	1 retrocopy	retro_pabe_2877,
Tupaia belangeri	ENSTBEG00000006477	4 retrocopies	retro_tbel_2646, retro_tbel_3572, retro_tbel_852 , retro_tbel_993,