RetrogeneDB ID: retro_tbel_3944

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_4303:3520..4189(-)
• 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_3944
ATGCATGAGATCATGCACATTCCAGGCCGGCCAGTGCAGCAACCAGATCTGCGCCAAGTTTTGGGAGGTTATCAGTGATG
AACCCGGTATCGACTCCACTGGCAGTTACCATGGAGACAGTGATTTGCAGCTGGAAAGAATCAATGTGTACTACAATGAA
GCCACTGGTAACAAATATGTGTCCCGGGCTATCCTGGTGGATCTGGAAGCTGGCACCATGGACTCAGTGCGGTCTGGACC
ATTTGGCTAGATCTTCAGGCCAGACAACTTCGTGTTCGGCCAGAGTAGTGCTGGGAACAACTGGGCCAAGGGCCACTACA
CAGAGGGGGCCGAGCTGCTCAACTCGGTCCTGGACGTGGTGAGGAAGGAGTCAGAAAGCTGTGACTGTCTCCAGGGCTTC
CAGCTGACCCACTCACTGGAAGGTGGCACTGGGTCAGGCATGGGCACCCTGCTCATCAGCAAGATCCGTGAGGAGTACCT
GGACAGCATCATGAACACCTTCAGCGTCATGCCCTCACCCAAGGTGTCCGACATGGTGGTGGAGCCCTACAACGCCACCC
TGTCTGTGCACCAGCTGGTGGAGAACACTACGAGACCTACTACATTGACAATGAGGCCCTGTACGACATCTGCTTCCGCA
CCTTGAAGCTGACCACACCCACCTACGGG

Alignment

ORF - retro_tbel_3944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.11 %
• Parental protein coverage: 50.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHI-QAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLE
          M.EI.HI.QAGQC.NQI.AKFWEVISDE.GID.TGSYHGDSDLQLERINVYYNEATGNKYV.RAILVDLE
Retrocopy MHEIMHI>QAGQCSNQICAKFWEVISDEPGIDSTGSYHGDSDLQLERINVYYNEATGNKYVSRAILVDLE

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSL
          .GTMDSVRSGPFG.IFRPDNFVFGQS.AGNNWAKGHYTEGAEL..SVLDVVRKESESCDCLQGFQLTHSL
Retrocopy AGTMDSVRSGPFG*IFRPDNFVFGQSSAGNNWAKGHYTEGAELLNSVLDVVRKESESCDCLQGFQLTHSL

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTD-ETYCIDNEALY
          .GGTGSGMGTLLISKIREEY.D.IMNTFSVMPSPKVSD.VVEPYNATLSVHQLVENT..ETY.IDNEALY
Retrocopy EGGTGSGMGTLLISKIREEYLDSIMNTFSVMPSPKVSDMVVEPYNATLSVHQLVENTT<ETYYIDNEALY

Parental  DICFRTLKLTTPTYG
          DICFRTLKLTTPTYG
Retrocopy DICFRTLKLTTPTYG

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_3944 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3944 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,