RetrogeneDB ID: retro_tbel_2948

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_124860:11536..12021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT5
• Ensembl ID: ENSTBEG00000013084
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 5 [Source:HGNC Symbol;Acc:20886]

Sequence

>retro_tbel_2948
AACGTGCTGACGCCAAGAATAAAGGCAAGTCATGTTGCTTTTGATTCTATGAAGAATTATTTAGATGCTATTTATGATGT
TACAGTGGTTTATGAAGGAAAAGACAGTAAAAGGCAGCGAATAGAACCACTGTCCATGACTGACTTTCTCTGCAAAGAAT
GTCCAAAAATTCATATTCATATTGATCGTATAGACAAAAAAGATGTCCCAGAAGAACAAGCATATATGAGAAGATGGTTT
CACGGACATTTTGAGATAAAGGATAAGTTGCTTATAGAATTCTATGATTCACCACATCCAGAAAGAAGAAATAAATTTCC
TGGGGAAACTGTTAATTCCAAACTAAGTCTTAAGACTTTACCATCAATATTGTTCTTAAGTGGTTTGACTGTTGCCATGC
TTTGACCAAGGCTGGAAGGAAACTGTATGTGAGTACGTGGCTATATGGGACCTTATTTGGCTGCCTGTGGGTTTCTATCA
AAGCA

Alignment

ORF - retro_tbel_2948 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.46 %
• Parental protein coverage: 50.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HVLTPRIKATHVAFDSMKNYLDAIYDVTVVYEGKDSKGQRIEPLSMTDFLCKECPKIHIHIDRIDKKDVP
          .VLTPRIKA.HVAFDSMKNYLDAIYDVTVVYEGKDSK.QRIEPLSMTDFLCKECPKIHIHIDRIDKKDVP
Retrocopy NVLTPRIKASHVAFDSMKNYLDAIYDVTVVYEGKDSKRQRIEPLSMTDFLCKECPKIHIHIDRIDKKDVP

Parental  EEQAYMRRWLHERFEIKDKLLIEFYDSPDPERRNKFPGESVNSKLSLKKTLPSVLILSGLTVAML-MTKT
          EEQAYMRRW.H..FEIKDKLLIEFYDSP.PERRNKFPGE.VNSKLSL.KTLPS.L.LSGLTVAML..TK.
Retrocopy EEQAYMRRWFHGHFEIKDKLLIEFYDSPHPERRNKFPGETVNSKLSL-KTLPSILFLSGLTVAML<LTKA

Parental  GRKLYVSTWLYGTLFGCLWVSIKA
          GRKLYVSTWLYGTLFGCLWVSIKA
Retrocopy GRKLYVSTWLYGTLFGCLWVSIKA

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_2948 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2948 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005142	1 retrocopy	retro_chof_376,
Dasypus novemcinctus	ENSDNOG00000004979	1 retrocopy	retro_dnov_823,
Dipodomys ordii	ENSDORG00000008708	1 retrocopy	retro_dord_523,
Otolemur garnettii	ENSOGAG00000008958	1 retrocopy	retro_ogar_3477,
Ochotona princeps	ENSOPRG00000014343	3 retrocopies	retro_opri_343, retro_opri_829, retro_opri_935,
Pongo abelii	ENSPPYG00000018320	1 retrocopy	retro_pabe_3671,
Sarcophilus harrisii	ENSSHAG00000000051	1 retrocopy	retro_shar_687,
Tupaia belangeri	ENSTBEG00000013084	1 retrocopy	retro_tbel_2948 ,