RetrogeneDB ID: retro_tsyr_1951

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_71388:5345..6375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHB
• Ensembl ID: ENSTSYG00000003570
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit [Source:HGNC Symbol;Acc:4803]

Sequence

>retro_tsyr_1951
ATCTTGACTTACTCTTTTAAAAATCTGCCCAGTACATCAAAATGGGCCCTCAAATTTTCCTTAAGACCTCTGAGTTGTTC
CTTCCAGCTAAGAACTGCCCCAGCTGTCCAGACCAAATCAAAGAAGACCTTAGCCAAACCCAATATAAGGAATATTGTGG
TAGTGGATGGTGTTCGCACTCCAGTTTTTGTTGTCAGGAGCTTCAGATAAAGACCTGAGGCCACGTGACTTGGCGAGAGC
AGCGCTTACGAGTTTGTTGCACAGGACCAATGTCCCAAAGGAAGTTGTTGATTATATCATCTTTGGCACAGTTATTCAGG
AGATGAAAGCAAGCAATGTGGTAGAGGCTGCCCTCAGAGCTGGCTTCTCTGACAAGATTCCTGCTCACACTGTCACCACG
GCTTGCATCTCTGCCAACCAAGCCATGACCACAGGTGTTGGCTTGATTGCTTCTGGCCAGTGTGGTGTGATTGTGGCAGG
TGGTGTCGAGTTAATGTCCGATGTTCCTGTTTGTCATTCAAGAAAACTGAGGAAAATGATGCTTGATCTCAACAAGGCCA
AGACTCGGGGCCAGCAACTATCTTTACTCTATAAATTCAGATTGAATTTCCTATCACCTGAGCTCCCTGTGGTGGCTGAG
TTCTCCACCAGCGAGACGATGGGCCACTCGGCAGACCAGCTGGCCATTGCCATGCCATGTTTCTCGACTGGAACAGGATG
ACTATGCACTGCGTTCTCACAATCTGTCTAAGAAGGCATAGGATGAAGGACTCCTTTCTGATGTACTCTTCAGTGTACCA
GAAAAAGATACAGTTACTAAAGATAATGGCATCCGTCCTTCCTCTCTGGAGAGATGGCCAAACTAAAATCTATGTTCATC
AAGCCTTATGGCACAGTGACAGCTGCAAACCCTTCTTTCCTGACTGATGGTGCATCTGCAATGCTGATTATGGCAGAGGA
AAAAGCTCTGGCCACAAGTTATAAGCCGAAGGCATATCTGAGGGACTTCATGTATGTGTCTCAGGATCCA

Alignment

ORF - retro_tsyr_1951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 72.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ILTYSFKNLPSTSKWALIPPHSLRPLSCSSQVRAAPAVQTKSKKTLAKPNIRNIVVVDGVRTP-FLLSGT
          ILTYSFKNLPSTSKWAL....SLRPLSCS.Q.R.APAVQTKSKKTLAKPNIRNIVVVDGVRTP.FLLSG.
Retrocopy ILTYSFKNLPSTSKWAL--KFSLRPLSCSFQLRTAPAVQTKSKKTLAKPNIRNIVVVDGVRTP>FLLSGA

Parental  SYKDLMPHDLARAALTGLLHRTNVPKEVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMACI
          S.KDL.P.DLARAALT.LLHRTNVPKEVVDYIIFGTVIQE.K.SNV..EAAL.AGFSDK.PAHTVT.ACI
Retrocopy SDKDLRPRDLARAALTSLLHRTNVPKEVVDYIIFGTVIQEMKASNVV-EAALRAGFSDKIPAHTVTTACI

Parental  SANQAMTTGVGLLTSGQCDVIVAGGVELMSDVPIRHSRKMRKMMLDLNKAKTLGQRLSLLSKFRLNFLSP
          SANQAMTTGVGL..SGQC.VIVAGGVELMSDVP..HSRK.RKMMLDLNKAKT.GQ.LSLL.KFRLNFLSP
Retrocopy SANQAMTTGVGLIASGQCGVIVAGGVELMSDVPVCHSRKLRKMMLDLNKAKTRGQQLSLLYKFRLNFLSP

Parental  ELPAVAEFSTSETMGHSADRLAAAFA-VSRLEQDEYALRSHSLAKKAQDEGLLSDVVPFSVPGKDTITKD
          ELP.VAEFSTSETMGHSAD.LA.A...VSRLEQD.YALRSH.L.KKA.DEGLLSDV..FSVP.KDT.TKD
Retrocopy ELPVVAEFSTSETMGHSADQLAIAMP>VSRLEQDDYALRSHNLSKKA*DEGLLSDVL-FSVPEKDTVTKD

Parental  NGIRPSSLE-QMAKLKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEKALAMGYKPKAYLRDFMYVSQDP
          NGIRPSSLE..MAKLK..FIKPYGTVTAAN.SFLTDGASAMLIMAEEKALA..YKPKAYLRDFMYVSQDP
Retrocopy NGIRPSSLE<EMAKLKSMFIKPYGTVTAANPSFLTDGASAMLIMAEEKALATSYKPKAYLRDFMYVSQDP

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_1951 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002288	1 retrocopy	retro_amel_1473,
Canis familiaris	ENSCAFG00000029395	1 retrocopy	retro_cfam_2114,
Choloepus hoffmanni	ENSCHOG00000010050	3 retrocopies	retro_chof_122, retro_chof_1869, retro_chof_911,
Homo sapiens	ENSG00000138029	1 retrocopy	retro_hsap_4778,
Gorilla gorilla	ENSGGOG00000025829	1 retrocopy	retro_ggor_2976,
Microcebus murinus	ENSMICG00000006750	1 retrocopy	retro_mmur_1315,
Mus musculus	ENSMUSG00000059447	2 retrocopies	retro_mmus_1427, retro_mmus_1961,
Otolemur garnettii	ENSOGAG00000005444	1 retrocopy	retro_ogar_167,
Pongo abelii	ENSPPYG00000012582	1 retrocopy	retro_pabe_3718,
Pan troglodytes	ENSPTRG00000011733	1 retrocopy	retro_ptro_3180,
Tarsius syrichta	ENSTSYG00000003570	2 retrocopies	retro_tsyr_1316, retro_tsyr_1951 ,