RetrogeneDB ID: retro_tbel_526

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2337:2748..3411(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEST
• Ensembl ID: ENSTBEG00000008404
• Aliases: None
• Description: mesoderm specific transcript [Source:HGNC Symbol;Acc:7028]

Sequence

>retro_tbel_526
CTGCACATCCCACCTCCTCAGCCTTCCCCTGCTCTTCATTCCTAAGAGTTTTCAAGCAAATTTTTTACCTACAAGGGACT
ACGCATCTTTTACCAAAACTCCATGGGTGTGGTTGGAAGTCCAGAAACCAGTGTGCTTCTACGCAGCTACCCAACATTCA
GCTATGACTGGTACAAGATTTGGGAAGATCTGACTCTGAGGGTTCATCAAGTAGTTACCCTTGATTTCTTAGGCTTTGAC
TTCTGTGACAAACTGAGACCCATCACTACACCATATTTGAGCAGGCCAGCATCGTGGAAGATTTTTGCAGCATCTGAGGC
TCCAAAACTGCATAATCAACCTCCTGCCTTGTGACTATGGATATATCATTGCTCAGGAGCTGCTCTGTTGGTACAAGCAG
AACTGTTCTACTTAGCTTACCATGAAGAGGCTTTGTGTGTCAAACACAGGTATCTCCCCTGAGATTCTCCATCCACTTCT
TCTCAGAAAGTTACTCAAAGGTGGAAGTGTGCTGTCACACATCCTCACTTGCTTGATGATCTTGTGTGTATTCTCTCAAG
GTTTTACCCAGTCTTTGGGACATACACGTGACCCTCTGAGAGTGAGCTGTTGGACATGTGGGCATGGATCCACAGCAATG
ACTGGAACTTGGTCATCCACAGT

Alignment

ORF - retro_tbel_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.67 %
• Parental protein coverage: 66.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LHIPPPQLSPALHSWKSSGKFFTY-GLRIFYQDSVGVVGSPEIAVLLHGFPTSSYDWYKIWEGLTLRFHR
          LHIPPPQ.SPALHS...S.KFFTY.GLRIFYQ.S.GVVGSPE..VLL...PT.SYDWYKIWE.LTLR.H.
Retrocopy LHIPPPQPSPALHS*EFSSKFFTYKGLRIFYQNSMGVVGSPETSVLLRSYPTFSYDWYKIWEDLTLRVHQ

Parental  VVALDFLGFGFSDKPRP-HHYSIFEQASIVE-ALLRHLGLQNRRINLLSHDYGDIVAQELLYRYKQNRSG
          VV.LDFLGF.F.DK.RP.HHY.IFEQASIVE...L.HL.LQN..INLL..DYG.I.AQELL..YKQN.S.
Retrocopy VVTLDFLGFDFCDKLRP<HHYTIFEQASIVE<RFLQHLRLQNCIINLLPCDYGYIIAQELLCWYKQNCST

Parental  RLTIKSLCLSNGGIFPETHRPLLLQKLLKDGGVLSPILTRLMNFFVFSRGLT-PVFGPYTRPSESELWDM
          .LT.K.LC.SN.GI.PE...PLLL.KLLK.G.VLS.ILT.LM...VFS.G.T.PVFG.YT.PSESEL.DM
Retrocopy *LTMKRLCVSNTGISPEILHPLLLRKLLKGGSVLSHILTCLMILCVFSQGFT<PVFGTYT*PSESELLDM

Parental  WAGIRNNDGNLVIDS
          WA.I..ND.NLVI.S
Retrocopy WAWIHSNDWNLVIHS

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_526 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_526 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 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005659	2 retrocopies	retro_amel_1177, retro_amel_1874,
Callithrix jacchus	ENSCJAG00000010760	2 retrocopies	retro_cjac_1563, retro_cjac_3931,
Felis catus	ENSFCAG00000022984	5 retrocopies	retro_fcat_1067, retro_fcat_1645, retro_fcat_1693, retro_fcat_2004, retro_fcat_326,
Loxodonta africana	ENSLAFG00000006066	3 retrocopies	retro_lafr_578, retro_lafr_584, retro_lafr_748,
Macropus eugenii	ENSMEUG00000008227	1 retrocopy	retro_meug_885,
Macaca mulatta	ENSMMUG00000009499	2 retrocopies	retro_mmul_1936, retro_mmul_94,
Sorex araneus	ENSSARG00000000502	1 retrocopy	retro_sara_352,
Tupaia belangeri	ENSTBEG00000008404	2 retrocopies	retro_tbel_1480, retro_tbel_526 ,
Tursiops truncatus	ENSTTRG00000004934	4 retrocopies	retro_ttru_1026, retro_ttru_1115, retro_ttru_1133, retro_ttru_1907,