RetrogeneDB ID: retro_tbel_4457

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_84223:10096..10984(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F3
• Ensembl ID: ENSTBEG00000000171
• Aliases: None
• Description: E2F transcription factor 3 [Source:HGNC Symbol;Acc:3115]

Sequence

>retro_tbel_4457
GCGAAGTGAAGGCTGGAGTTGGGAGAGAGCGGTCACCAGTACCTCGCGGATGGTCTGAAAACCCCCAAGGGCAAAGTACA
CGGTGCACTTCGGAGTCCAGACAGTCCCCAAACTCCCAAATCTCCCTCAGAAAAAATGTGGTATGATACATCCCTCGGTC
TCCTCACCAAGAAGTTCATTCAGCTGCTGAGACAGTTGCCGACAGGGACTTGGATTTGAACAAGGCAGCGGAGGTGCTGA
AGGTGCAAAAGAGGAGGATCTATGACATCACCAACGTGCTGGAAGGCATCCACCTCATCAAGAAGAAGTCCAAAAACAAC
GTGCAGTGGATGGGCTGCAGTCTGTCTGAGGACCGGGGGAATGCTGGCCCAGTGTCAAGGCCTTTCCAAGGAAGTGACCG
AGGTCAGTCAGGAGAAGAAGTTAGACGAACTGATCCAAAGCTGCACCCTGGACCTCAAACTGTTAACCGAGGATTCAGAG
AATCAAAGGTTAGCTTAAGTTACATATCAAGATATTCGAAAAACTAGTGGCCTTAAAGACCAAGCTGTTATAGTCGTGAA
AGCCCCTCCAGAAACAAGACTTGAAGTGCCTGACCCAATAGATAGCCTACAAATACATTTGGCAAGTACCCAAGGACCCA
TTGAGGTTTACTTGTGTCCAGAAGAGACTGAAACACACAGTCTAATGAAAACAAACAACCAAGACCACAATGGGAATATC
CCCAAACCCACTTCCAAAGACTTGGCTTCAACCAACTCAGGACATAGTGATAGCTCCATTTCTATGGCTAGCCTTTCTCC
TTTGGCCTCCCCAGCCAATCTTTTACAGCAGACTGAAGACCAAATCCCTTCCAACCTGGAAGGGCCGTTTGTGAACTTAC
TGACCCCC

Alignment

ORF - retro_tbel_4457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.64 %
• Parental protein coverage: 65.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKRRLELGESGHQYLADGLKTPKGKGRGALRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQLLSQSPDGV
          AK.RLELGESGHQYLADGLKTPKGK..GALRSPDSP.TPKSPSEK..YDTSLGLLTKKFIQLL.Q.P.G.
Retrocopy AK*RLELGESGHQYLADGLKTPKGKVHGALRSPDSPQTPKSPSEKMWYDTSLGLLTKKFIQLLRQLPTGT

Parental  -LDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQWMGCSLSED-GGMLAQCQGLSKEVTELSQE
          .LDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQWMGCSLSED.GGMLAQCQGLSKEVTE.SQE
Retrocopy <LDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQWMGCSLSED>GGMLAQCQGLSKEVTEVSQE

Parental  EKKLDELIQSCTLDLKLLTEDSENQRYPYVTYQDIRKTSGLKDQTVIVVKAPPETRLEVPDPIESLQIH-
          .KKLDELIQSCTLDLKLLTEDSENQR...VTYQDIRKTSGLKDQ.VIVVKAPPETRLEVPDPI.SLQIH.
Retrocopy -KKLDELIQSCTLDLKLLTEDSENQRLA*VTYQDIRKTSGLKDQAVIVVKAPPETRLEVPDPIDSLQIHL

Parental  ASTQGPIEVYLCPEETETHSPMKTNNQDHNGNIPKPTSKDLASTNSGHSDSSISMASLSPLASPANLLQQ
          ASTQGPIEVYLCPEETETHS.MKTNNQDHNGNIPKPTSKDLASTNSGHSDSSISMASLSPLASPANLLQQ
Retrocopy ASTQGPIEVYLCPEETETHSLMKTNNQDHNGNIPKPTSKDLASTNSGHSDSSISMASLSPLASPANLLQQ

Parental  TEDQIPSNLEGPFVNLLPP
          TEDQIPSNLEGPFVNLL.P
Retrocopy TEDQIPSNLEGPFVNLLTP

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_4457 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4457 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021045	1 retrocopy	retro_btau_1523,
Choloepus hoffmanni	ENSCHOG00000008679	2 retrocopies	retro_chof_416, retro_chof_871,
Homo sapiens	ENSG00000112242	1 retrocopy	retro_hsap_1749,
Gorilla gorilla	ENSGGOG00000011022	2 retrocopies	retro_ggor_1796, retro_ggor_2254,
Macaca mulatta	ENSMMUG00000017649	1 retrocopy	retro_mmul_955,
Pongo abelii	ENSPPYG00000016269	2 retrocopies	retro_pabe_1447, retro_pabe_2137,
Pan troglodytes	ENSPTRG00000023584	2 retrocopies	retro_ptro_1217, retro_ptro_1731,
Tupaia belangeri	ENSTBEG00000000171	1 retrocopy	retro_tbel_4457 ,