RetrogeneDB ID: retro_tbel_2477

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_111566:17194..17967(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MNS1
• Ensembl ID: ENSTBEG00000004372
• Aliases: None
• Description: meiosis-specific nuclear structural 1 [Source:HGNC Symbol;Acc:29636]

Sequence

>retro_tbel_2477
GTAGATGATAACTACCGCAAAAAAATTGCATTTCTAGGAGCTAAAAAAAATATACAGAGTCAAGTCAGGAACCAAATGGT
GCAGAATGGAAATGATACCCATGGTGAACACAAGAGATTTCAGAATGAACAATTTGAGTTGGATATGGAAGAGGCCATTC
AAAAGGCAGAAGAAAATAAGAGATTGAGGAAACTCCAGCTTGAACAAGAAGAAAAATTGGCTATGGAACTAGCAAAACTA
AAACATGAAAGTCTAAAGGATGAAAAGATGAGACAACAAGTAAGAGAAAACAGTATCGAGCTCAGAGAATTAGAGAAAAA
GTTAAAAGCAGCTTACATGAATAAAGAAAGGGCAGCTCAGATTGCTGAAAAGATGCCATTAAATATGAGCAAATGAAACG
TGATGCTGAAATAGCCAAAACCATGATGGAAGAACAGGAGCGAGTAATAAAGGAAGAGAGTGCCGCCGAAGACAAACGGA
ACGAAGTGAAGGCACAAAACTATTTTGACTTAGAGAAACAAGTTGAAGAGCCAGAGAGAAAAAAGCAAGAAACTTATGAA
CAGTTGTTGAAAGAAAAACTCATGATTGATGAAATTGTTAGGAAAATCTATGAAGAAGATCAACTAGAAAAACAACACAA
ATTAGAAAAAATGAATGCCACTCGAAGGTATATAGAAGAGTTTCAGAAAGAGCAGGCTCTCTGGAGAAAGAAGAAACGTG
AGGAGATGGAAGAAGAAAACAGAAAAATCATAGAATTTGCCCACATACAGCAG

Alignment

ORF - retro_tbel_2477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.4 %
• Parental protein coverage: 53.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDDNYRKKL-HVQELKNIQSQVRNQMVQNGNDTRVEHKRFLRLLQNEQFELDMEEAIQKAEENKRLRKLQ
          VDDNYRKK.........IQSQVRNQMVQNGNDT..EHKRF....QNEQFELDMEEAIQKAEENKRLRKLQ
Retrocopy VDDNYRKKIAFLGAXXXIQSQVRNQMVQNGNDTHGEHKRF----QNEQFELDMEEAIQKAEENKRLRKLQ

Parental  LEQEEKLAMELAKLKHESLKDEKMRQQVRENSIELRELEKKLKAAYMNKERAAQIAEK-DAIKYEQMKRD
          LEQEEKLAMELAKLKHESLKDEKMRQQVRENSIELRELEKKLKAAYMNKERAAQIAEK.DAIKYEQMKRD
Retrocopy LEQEEKLAMELAKLKHESLKDEKMRQQVRENSIELRELEKKLKAAYMNKERAAQIAEK<DAIKYEQMKRD

Parental  AEIAKTMMEEQERVIKEESAAEDKRNKVKAQYYFDLEKQVEEQERKKQEAYEQLLKEKLMIDEIVRKIYE
          AEIAKTMMEEQERVIKEESAAEDKRN.VKAQ.YFDLEKQVEE.ERKKQE.YEQLLKEKLMIDEIVRKIYE
Retrocopy AEIAKTMMEEQERVIKEESAAEDKRNEVKAQNYFDLEKQVEEPERKKQETYEQLLKEKLMIDEIVRKIYE

Parental  EDQLEKQHKLEKMNATRRYIEEFQKEQALWRKKKREEMEEENRKIIEFAHIQQ
          EDQLEKQHKLEKMNATRRYIEEFQKEQALWRKKKREEMEEENRKIIEFAHIQQ
Retrocopy EDQLEKQHKLEKMNATRRYIEEFQKEQALWRKKKREEMEEENRKIIEFAHIQQ

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_2477 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2477 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016053	1 retrocopy	retro_cfam_1255,
Tupaia belangeri	ENSTBEG00000004372	3 retrocopies	retro_tbel_1821, retro_tbel_2477 , retro_tbel_2534,