RetrogeneDB ID: retro_tsyr_1269

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_373259:36..956(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX5
• Ensembl ID: ENSTSYG00000012149
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 5 [Source:HGNC Symbol;Acc:2746]

Sequence

>retro_tsyr_1269
GGGTTGGCTATGGTTGGAGTAGCACAGTTCTCTTATTTGCCGCCTGCCATTGTCCACATCAACCATCAGCCATTCCTAGA
GAGAGGTGATGGGCCTATCTGCTTGGTGCTGGCACCAACCCAGGAACTGGCCCAGCAGGTGCAGCAGGTGGTTGTTGAAG
ACTGTAGAGCCTGTCGCCTGAAGTCCACATGCATCTATGGCGGTGCTCCCAAAGGATCACAGATACGGGACTTGGAGAGA
GGTGTGGAAATCTGTATTGCAACACCAGGAAGACTGATTGACTTTTTAGAGTGTGGGAAAACCAACCTAAGAAGAACACT
CTATCTTGTCCTTGATGAAGCAGATAGAATGCTTGATATGGGCTTTGAACCCCAAATAAGGAAGATTGTTGATCAGATAA
GACCTGATAGGCAAACCCTAATGTGAAGTGCGACCTGGCCAAAGAAGGCAGGCAGCTTGCCGAAGATTTCCTGAAGGACT
ATATTCACATGAACACTGGTGCACTAGAACTGAGTGCAAACCACAACATTCTCCAAATTGTGGATGTGTATCATGATGTA
GAAAACGATGAAAAACGTATTCGTCTAATGGAAGAGATCATGAGTGAGGAGAGTAAAACCATTGCTTTTGTTGAAACCAA
AAGAAGATGTGATGAGTTTACCAGAAAAATGAGGAGAGATGGGTGACCTGCCATGGGTATCCATGGTGACAAGAGTCAAC
AGGAACGTGACTGGGTTCTAAATGAATTCAAACATGGAAAAACTCCTATTCTGATTGCTACAGATGTGACCTCCAGAGGG
CTAGATGTGGAAGATGTGAAATTTGTTATCAATTATGACTACCCTAACTCCTCAGAGGATTATATTCATGGAATTGGAAG
AACTGCTCGCAGTATCAAAACAGGCACAGCATACACATTC

Alignment

ORF - retro_tsyr_1269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.35 %
• Parental protein coverage: 50.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGA
          G.A..G.....SYL.PAIVHINHQPFLERGDGPICLVLAPT.ELAQQVQQV..E.CRACRLKSTCIYGGA
Retrocopy GLAMVGVAQ-FSYLPPAIVHINHQPFLERGDGPICLVLAPTQELAQQVQQVVVEDCRACRLKSTCIYGGA

Parental  PKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQT
          PKG.QIRDLERGVEICIATPGRLIDFLECGKTNLRRT.YLVLDEADRMLDMGFEPQIRKIVDQIRPDRQT
Retrocopy PKGSQIRDLERGVEICIATPGRLIDFLECGKTNLRRTLYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQT

Parental  LMWSATWP-KEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKT
          LM.SATWP.KE.RQLAEDFLKDYIH.N.GALELSANHNILQIVDV.HDVE.DEK.IRLMEEIMSE.E.KT
Retrocopy LM*SATWP<KEGRQLAEDFLKDYIHMNTGALELSANHNILQIVDVYHDVENDEKRIRLMEEIMSE-ESKT

Parental  IVFVETKRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVI
          I.FVETKRRCDE.TRKMRRDG.PAMGIHGDKSQQERDWVLNEFKHGK.PILIATDV.SRGLDVEDVKFVI
Retrocopy IAFVETKRRCDEFTRKMRRDG*PAMGIHGDKSQQERDWVLNEFKHGKTPILIATDVTSRGLDVEDVKFVI

Parental  NYDYPNSSKDYIHRIGRTARSTKTGTAYTF
          NYDYPNSS.DYIH.IGRTARS.KTGTAYTF
Retrocopy NYDYPNSSEDYIHGIGRTARSIKTGTAYTF

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_1269 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019950	1 retrocopy	retro_etel_1009,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172,
Myotis lucifugus	ENSMLUG00000009496	4 retrocopies	retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788,
Pteropus vampyrus	ENSPVAG00000001932	1 retrocopy	retro_pvam_1267,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260,
Tarsius syrichta	ENSTSYG00000012149	1 retrocopy	retro_tsyr_1269 ,
Tursiops truncatus	ENSTTRG00000008793	1 retrocopy	retro_ttru_1662,