RetrogeneDB ID: retro_tbel_4103

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_6733:113009..113695(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MNAT1
• Ensembl ID: ENSTBEG00000005536
• Aliases: None
• Description: menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis) [Source:HGNC Symbol;Acc:7181]

Sequence

>retro_tbel_4103
GGAGCTGGCAATTGTCCTGAGTGTGGCACTCCACTTAGAAAGAGCAACTTCAGGGTACAACTCTTTGAAGATCCTGCTGT
TGACAAAGAGGTGGAGATTCGAAAAAAAGTGCTAAAGATATACAATAAAAGGGAAGAAGATTTTCCTAGTCTAAGAGAAT
ATAATGATTTCCTGGAAGAAGTGGAAGAAATTGTTTTCAACTTGACCAACAATGTGGATTTGGATAACACTAAAAAGAAA
ATGGAGATATACCAAAAGGAAAACAAAGATGTCATTCAGAAAAATAAGTTAAAGATGACTCAGGAACAGGAAGAATTAGA
AGAAGCATTAGAAGTAGAACGTCAGGAAAATGAACAAAGAAGATTATCTATACAAAAAGAAGAACAACTGCAGCAAATTC
TAAAAAAGAAGAATAAACAGACTTTTTTAGATGAACTGGAGAGTTCAGATCTTCCTGTGGCTCTCCTCTTGGCTCAGCAT
AAAGACAGATCTACTCAACAGGAAATGCAACTCGAGAAACCAAGCCAAAAAAGCCAGTTGCATTTTCCACAGGCATCAAG
AATGGGTCAAATATTTCATTAGCACCTATTCACAAGCTTGAAGAACGCTCTGTGTGAATACCATCACTGCAAATAGGGCC
TTACGGACCACAGGTTCTGGAGCTCAAGGAGTAAGGAAGACTTGGG

Alignment

ORF - retro_tbel_4103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 82.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAGNCPECGTPLRKSNFRVQLFEDPAVDKEVEIRKKVLKIYNKKEEDFPSLREYNDFLEEVEEIVFNLTN
          GAGNCPECGTPLRKSNFRVQLFEDPAVDKEVEIRKKVLKIYNK.EEDFPSLREYNDFLEEVEEIVFNLTN
Retrocopy GAGNCPECGTPLRKSNFRVQLFEDPAVDKEVEIRKKVLKIYNKREEDFPSLREYNDFLEEVEEIVFNLTN

Parental  NVDLDNTKKKMKIYQKENKDVIQKNKLKMTREQEELEEALEVERQENEQRRLFIQKEEQLQQILKRKNKQ
          NVDLDNTKKKM.IYQKENKDVIQKNKLKMT.EQEELEEALEVERQENEQRRL.IQKEEQLQQILK.KNKQ
Retrocopy NVDLDNTKKKMEIYQKENKDVIQKNKLKMTQEQEELEEALEVERQENEQRRLSIQKEEQLQQILKKKNKQ

Parental  AFLDELESSDLPVALLLAQHKDRSTQLEMQLEKP-KPIKPVTFSTGIKMGQHISLAPIHKLEEALYEYQP
          .FLDELESSDLPVALLLAQHKDRSTQ.EMQLEKP.KP.KPV.FSTGIK.G..ISLAPIHKLEE.......
Retrocopy TFLDELESSDLPVALLLAQHKDRSTQQEMQLEKP<KPKKPVAFSTGIKNGSNISLAPIHKLEERSV*IPS

Parental  LQIETYGPQVPELEVLGRLG
          LQI..YGPQV.EL...GRLG
Retrocopy LQIGPYGPQVLELKE*GRLG

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_4103 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4103 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000005536	2 retrocopies	retro_tbel_2303, retro_tbel_4103 ,
Tursiops truncatus	ENSTTRG00000013838	1 retrocopy	retro_ttru_1348,