RetrogeneDB ID: retro_tsyr_338

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_974:17118..17599(-)
• Located in intron of: ENSTSYG00000003251

Retrocopy information

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

Parental gene information

• Parental gene symbol: AASDHPPT
• Ensembl ID: ENSTSYG00000005102
• Aliases: None
• Description: aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase [Source:HGNC Symbol;Acc:14235]

Sequence

>retro_tsyr_338
GGTTCAATGCCAGAATTCTTTCATATTATGAAAAAAAAAGTTTACCACCAAAGAATGGGAAACAATCAAAAGCTTTAAGG
ATGAATGGATTCAGCTGGATATGTTTTATAGAAATTGGGCATTCAAAGAAAGCTTCATAAAGGCCATTGGTGTTGGACTG
GGATTTGAACTGCAACAACTTGAATTTGATATATCTCTGTTAAACTTGGATATAGACCAAGTTTATAAAGAAACACGTTT
GTTCCCAAATGGAGAGGAAGAAAAAGATGTATGGGCATCTGAGGAAAGCAAAATAGATGGGCACCATTTTGTTGCCGTAG
CTCTTAGGAAACCCGATGGATCTAAACATCAGGATGTGCCATCTGAAGATGATTCTAAACCAACCCCAAGGCAGTTTACT
GTTCTCACCTTTAATGATTTAATAGCATCTGCTGTTCCCATGACACCTGAAGATCCTTTATTTTGGGACTGTTTTTGCTT
C

Alignment

ORF - retro_tsyr_338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 96.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSIPEFFHIMKRK-FTNKEWETIRSFKDEWTQLDMFYRNWALKESFIKAIGVGLGFELQRLEFDISPLNL
          GS.PEFFHIM....FT.KEWETI.SFKDEW.QLDMFYRNWA.KESFIKAIGVGLGFELQ.LEFDIS.LNL
Retrocopy GSMPEFFHIMXXX>FTTKEWETIKSFKDEWIQLDMFYRNWAFKESFIKAIGVGLGFELQQLEFDISLLNL

Parental  DIGQVYKETRLFLDGEEEKE-WAFEESKIDEHHFVAVALRKPDGSKHQDVPSQDDSKPTPRQFTVLTFND
          DI.QVYKETRLF..GEEEK..WA.EESKID.HHFVAVALRKPDGSKHQDVPS.DDSKPTPRQFTVLTFND
Retrocopy DIDQVYKETRLFPNGEEEKDVWASEESKIDGHHFVAVALRKPDGSKHQDVPSEDDSKPTPRQFTVLTFND

Parental  LISSAVPMTPEDPSFWDCFCF
          LI.SAVPMTPEDP.FWDCFCF
Retrocopy LIASAVPMTPEDPLFWDCFCF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_338 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012279	1 retrocopy	retro_btau_134,
Echinops telfairi	ENSETEG00000004248	2 retrocopies	retro_etel_1231, retro_etel_1503,
Myotis lucifugus	ENSMLUG00000016238	4 retrocopies	retro_mluc_1361, retro_mluc_1362, retro_mluc_1363, retro_mluc_479,
Mus musculus	ENSMUSG00000025894	1 retrocopy	retro_mmus_2827,
Oryctolagus cuniculus	ENSOCUG00000000231	1 retrocopy	retro_ocun_379,
Ictidomys tridecemlineatus	ENSSTOG00000000268	1 retrocopy	retro_itri_1438,
Tarsius syrichta	ENSTSYG00000005102	1 retrocopy	retro_tsyr_338 ,