RetrogeneDB ID: retro_tsyr_1752

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_56876:11455..12105(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA4
• Ensembl ID: ENSTSYG00000008600
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 4 [Source:HGNC Symbol;Acc:14885]

Sequence

>retro_tsyr_1752
AGATCGGTCGGGCATGGTGAAGCAGATCCAGACCTTGCGCCTGCCGTGGAGTGCAAGGGTCAGGGCGGGCGCAACAACCC
CCAAGGACCGCTGCAAGAGCTGCAGTGGCACCAAGGTGACCGGCGAGAAGAAGATTATCGAGATTCATGTTGAAAAGGGT
ACATGAAAGAGGGACAGAAGATATGTTTTATTCATGGAGAAGGAGACCAGGAGCCTGAACTGGAGCCTGGTGATGTCATC
AATGTGCTTGATCAGAAGGATCATAGTGTCTTTCAGAGATGAGGCCATAACTTGATCATGAAAATGAAAATTCAGCTTTC
TGAAGCTCTTTGTGGCTTCAAGAAGACGATAAAAACACGGAATGATCAAATACTTGTGATCACATCCAAAACAGGGGAGG
TAGCCAAGCACGGGGATCTGAAGTGTGTGCGCAATGAAGGAATGCTCATCTACAAGGCACCCCTGGAGAGGGACTCTGAT
CATCCAGTTTTTAGTCGTCTTTCCCAGAAAAACATTGGCTTTCTCCGGAAAAGCTTCCTCAGCTGGAAGCCCTGCTCCAT
CCTCGACAGAAAGTGAGGATTACAGAGGACATGGACCAGGTGGAGCTGAAGGCGTTTAACCCCAGCAAACAGAACTGGCG
CCAGTACCGG

Alignment

ORF - retro_tsyr_1752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.64 %
• Parental protein coverage: 58.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QQIGPGMVQQIQTVCVECKGQGERINP-KDRCESCSGAKVTREKKIIEVHVE-KG-MKDGQKILF-HGEG
          ...G.G.........VECKGQG.R.NP.KDRC.SCSG.KVT.EKKIIE.HVE.KG.MK.GQKI.F.HGEG
Retrocopy RSVGHGEADPDLAPAVECKGQGGRNNP>KDRCKSCSGTKVTGEKKIIEIHVE<KGYMKEGQKICFIHGEG

Parental  DQEPELEPGDVIIVLDQKDHSVFQRRGHDLVMKMKIQLSEALCGFKKTIKTLDDRTLVITSKSXXXXXXX
          DQEPELEPGDVI.VLDQKDHSVFQR.GH.L.MKMKIQLSEALCGFKKTIKT..D..LVITSK........
Retrocopy DQEPELEPGDVINVLDQKDHSVFQR*GHNLIMKMKIQLSEALCGFKKTIKTRNDQILVITSKTGEVAKHG

Parental  XXXCVHKKGMPIYKA-PERGTLIIQF-VIF-PEKHWLSPEKLPQLEALLPPRQTVRITEDMDQVELKEFN
          ...CV...GM.IYKA.P.RGTLIIQF.V.F.PEKHWLSPEKLPQLEALL.PRQ.VRITEDMDQVELK.FN
Retrocopy DLKCVRNEGMLIYKA>PWRGTLIIQFLVVF>PEKHWLSPEKLPQLEALLHPRQKVRITEDMDQVELKAFN

Parental  PSEQNWRQHR
          PS.QNWRQ.R
Retrocopy PSKQNWRQYR

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_1752 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 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012576	1 retrocopy	retro_amel_1659,
Dipodomys ordii	ENSDORG00000005972	4 retrocopies	retro_dord_245, retro_dord_280, retro_dord_333, retro_dord_533,
Echinops telfairi	ENSETEG00000004320	4 retrocopies	retro_etel_1010, retro_etel_1031, retro_etel_1067, retro_etel_608,
Macropus eugenii	ENSMEUG00000015982	4 retrocopies	retro_meug_1059, retro_meug_1893, retro_meug_292, retro_meug_624,
Microcebus murinus	ENSMICG00000008789	6 retrocopies	retro_mmur_1242, retro_mmur_1460, retro_mmur_39, retro_mmur_482, retro_mmur_496, retro_mmur_578,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
Otolemur garnettii	ENSOGAG00000006752	5 retrocopies	retro_ogar_1760, retro_ogar_1985, retro_ogar_221, retro_ogar_2656, retro_ogar_841,
Ochotona princeps	ENSOPRG00000007594	1 retrocopy	retro_opri_1028,
Tupaia belangeri	ENSTBEG00000009268	9 retrocopies	retro_tbel_2276, retro_tbel_2308, retro_tbel_2790, retro_tbel_2831, retro_tbel_3242, retro_tbel_4322, retro_tbel_4735, retro_tbel_772, retro_tbel_796,
Tarsius syrichta	ENSTSYG00000001329	4 retrocopies	retro_tsyr_110, retro_tsyr_1384, retro_tsyr_1921, retro_tsyr_57,
Tarsius syrichta	ENSTSYG00000008600	1 retrocopy	retro_tsyr_1752 ,