RetrogeneDB ID: retro_tbel_2291

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_108621:260304..261055(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000004854
• Aliases: None
• Description: None

Sequence

>retro_tbel_2291
ATGCATGAGATCGTGCACATCCAGGCTGGCCAGTGCAGCAACCAGATCGGCGCCAAGTTTTGGTACGTTATCAGTGATGA
ACACGATATCGACCCCACTGACAGTTACCGTGGAGACAGTGATTTGCAGCTGGAAAGAATCAATGTGTACTACAATGAAG
CCACTGGTAACAAATACATGCCCCGGGCTATTCTGGTGGATCTGGAACCTGGCACCATGGACTCAGTGCGGTCTGGACCA
TTTGGCTAGATCTTCAGGCCAGACAACTTCGTGTTCGGCCAGAGTGGTGCTGGGAACAACTGGGCCAAGGGCCACTACAC
AGAGGGGGCCGAACTGGTCAACTCGGTCCTGGACGTGGTGAGGAAGGAGTCAGAAAGCTGTGACTGTCTCCAAGGCTTCC
AGCTGACCCACTCACTGGGAGGTGGCACCGGGTCAGGCATGGGCACCCTGCTCATCAGCCAGATCCGTGAGGAGTACCGG
GACCGCATCATGAACACCTTCAGCGTCATGCCCTCACCCAAGGTGTTGGACACGGTGGTGGAGCCCTACAACGCCACCCT
GTCCGTGCACCAGCTGGTGGAGAACACTGACGAGTCCTACTGCATTGACAAGGAGGCCCTGTACAGACATCTGCTTCCGC
ACCCTGAAGCTGAGCACACCCACCTACGGGGACCTCCACCACCTGGTGTCGGCCACCATGAGCAGCGTCACCACCTGTCT
GCGCTTCCCGGGCCAGCTGAAGGCCGACTTG

Alignment

ORF - retro_tbel_2291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.03 %
• Parental protein coverage: 56.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEP
          M.EIVHIQAGQC.NQIGAKFW.VISDEH.IDPT.SY.GDSDLQLERINVYYNEATGNKY.PRAILVDLEP
Retrocopy MHEIVHIQAGQCSNQIGAKFWYVISDEHDIDPTDSYRGDSDLQLERINVYYNEATGNKYMPRAILVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLG
          GTMDSVRSGPFG.IFRPDNFVFGQSGAGNNWAKGHYTEGAELV.SVLDVVRKESESCDCLQGFQLTHSLG
Retrocopy GTMDSVRSGPFG*IFRPDNFVFGQSGAGNNWAKGHYTEGAELVNSVLDVVRKESESCDCLQGFQLTHSLG

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY-D
          GGTGSGMGTLLIS.IREEY.DRIMNTFSVMPSPKV.DTVVEPYNATLSVHQLVENTDE.YCID.EALY.D
Retrocopy GGTGSGMGTLLISQIREEYRDRIMNTFSVMPSPKVLDTVVEPYNATLSVHQLVENTDESYCIDKEALY>D

Parental  ICFRTLKLTTPTYGDL-NLVSATMSGVTTCLRFPGQLNADL
          ICFRTLKL.TPTYGDL..LVSATMS.VTTCLRFPGQL.ADL
Retrocopy ICFRTLKLSTPTYGDLHHLVSATMSSVTTCLRFPGQLKADL

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_2291 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2291 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 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017637	1 retrocopy	retro_cjac_1649,
Erinaceus europaeus	ENSEEUG00000002955	1 retrocopy	retro_eeur_441,
Myotis lucifugus	ENSMLUG00000016179	1 retrocopy	retro_mluc_401,
Tupaia belangeri	ENSTBEG00000004854	9 retrocopies	retro_tbel_2291 , retro_tbel_3456, retro_tbel_3944, retro_tbel_4113, retro_tbel_413, retro_tbel_4390, retro_tbel_4439, retro_tbel_961, retro_tbel_962,
Tarsius syrichta	ENSTSYG00000003440	2 retrocopies	retro_tsyr_1068, retro_tsyr_2125,
Tursiops truncatus	ENSTTRG00000006144	1 retrocopy	retro_ttru_1393,