RetrogeneDB ID: retro_tbel_3933

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_40767:285..797(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000005834
• Aliases: None
• Description: None

Sequence

>retro_tbel_3933
CCCAGGTGACTCTCAGACCAGCGTCAGCACCATGTGGCTGACTGTGACTTCAGAGGCAGTGTGGGCTCCCAGTCCAGAGG
GCAGCTGCTGCTGCTGTCCAACCTGCACCCCAGCGTGTCCGACAGGGATATCCAGATGCTCTTTGGCGAATTCGGAGAGC
TGCAGAAGCAGGCAGCGGTGCACTACGATGGCTCTGGCCGCAGCTTGGGCACAGCCACCGTGCACTTCCAGTGGAAGGCT
AATGCCCTGAAGGTGCTGAGGGAGTACAACGGTGTCCCTTTGGATGACTGCCCCTTGAGCATCCAGGTGGTCACCTCGCC
TGGGGATACACCGAGGAGACCCATCTCCAGTGGGAACGGAGGCAGCCTAAGCGGGAAGCACCACTCAGGAGGTTCAGCCC
ATGGGTGCAGCTTCTGGCGAGGCAGCAGGAGAGGACAGCAAGTCCCAGGCCACCATTCAAAGCAGCAGCTTGTGCAGAGG
AACTGGACACCCAACTCGACGCCTACAAAGCT

Alignment

ORF - retro_tbel_3933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.11 %
• Parental protein coverage: 97.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PKQLPDKWQHDLFDSGFGGGAGVETGGKLLV-SNLDFGVSDADIQELFAEFGTLKK-AAVHYDRSGRSLG
          P..L.D..QH...D..F.G..G....G.LL..SNL...VSD.DIQ.LF.EFG.L.K.AAVHYD.SGRSLG
Retrocopy PR*LSDQRQHHVADCDFRGSVGSQSRGQLLLLSNLHPSVSDRDIQMLFGEFGELQKQAAVHYDGSGRSLG

Parental  TADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQIDTQRRPVQSVNRGGMTRTRGSGGFGGGGGTRR
          TA.VHF..KA.ALK....YNGVPLD..P..IQ.VTS..DT.RRP..S.N.G.......SGG...G....R
Retrocopy TATVHFQWKANALKVLREYNGVPLDDCPLSIQVVTSPGDTPRRPISSGNGGSLSGKHHSGGSAHGCSFWR

Parental  GSRGGSRGRGRGTGRSSKQQL-SAEELDAQLDAYNA
          GSR.G....G......SKQQL..AEELD.QLDAY.A
Retrocopy GSRRGQQVPG----HHSKQQL<CAEELDTQLDAYKA

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_3933 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3933 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005877	1 retrocopy	retro_cfam_1395,
Gorilla gorilla	ENSGGOG00000013935	1 retrocopy	retro_ggor_2523,
Macaca mulatta	ENSMMUG00000012884	1 retrocopy	retro_mmul_1679,
Mus musculus	ENSMUSG00000025134	1 retrocopy	retro_mmus_286,
Sarcophilus harrisii	ENSSHAG00000010459	1 retrocopy	retro_shar_332,
Tupaia belangeri	ENSTBEG00000005834	7 retrocopies	retro_tbel_237, retro_tbel_2432, retro_tbel_251, retro_tbel_2690, retro_tbel_2918, retro_tbel_3933 , retro_tbel_3934,