RetrogeneDB ID: retro_tsyr_1986

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_75066:8530..9125(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000004067
• Aliases: None
• Description: None

Sequence

>retro_tsyr_1986
TACCAGTACTGTTAAGAACAAGCAGTACCCAAAGTCTTACTTCCATAGAGGTGTTTCAGATGCCAAGATTTGCTTCTTTA
GCCTGGGGTGGAAGAAGGCAAAAATGGATGAGTTTCCACTCTATAGCCACATGGTGTCAGATGAATATGAGCAGCTTTCC
TCAGGCACCCTGGAGGCTGCCTGTGTTTGTGCCAACTGCTACATAATAAAAAGTTGTGGCAAAGATGACTTTCATATTCA
AGTGTGACTGCATCTCTTTGATATCATTCACATCAACAAGATGTCCTGTGTGGGGGCTCACTGGCTCCAGATCGGTGTGC
AAGGTACCTTGGAAAGCCCCAGAGCACTGTGGCTAGCATGCTCATTGACCAAGTCATCGTATCCATTCACATCAAGTTGC
AGAACAAGGGGCACGTGATTGAGAGGCTGTGCGGGGCCAAGTTCAAGTTCCCTGGTCACCAAAAGATCTGCATCTCAAAG
AAGTGAGGCTTTACCAAGAAAATACCGACAGATTTGAAGACATGTTGGCTGAGAAGCAGCTCATCCCAGATGGCTGTGGG
GTCAAATACATCCCCAATATGGTCCCTTGGACAAG

Alignment

ORF - retro_tsyr_1986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 87.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YRYC-KNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMV
          Y.YC.KNK.YPKS.F.RGV.DAKI..F.LG.KKAK.DEFPL..HMVSDEYEQLSS..LEAA..CAN.Y..
Retrocopy YQYC>KNKQYPKSYFHRGVSDAKICFFSLGWKKAKMDEFPLYSHMVSDEYEQLSSGTLEAACVCANCYII

Parental  KSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGA-FGKPQGTVARVHIGQVIMSIRTKLQNKE
          KSCGKD.FHI.V.LH.F..I.INKM.SC.GA..LQ.G..G...GKPQ.TVA...I.QVI.SI..KLQNK.
Retrocopy KSCGKDDFHIQV*LHLFDIIHINKM-SCVGAHWLQIGVQGT<LGKPQSTVASMLIDQVIVSIHIKLQNKG

Parental  HVIEALRRAKFKFPGRQKIHISKKWGFTK-FNADEFEDMVAEKRLIPDGCGVKYIPNR-GPLDK
          HVIE.L..AKFKFPG.QKI.ISKK.GFTK..N.D.FEDM.AEK.LIPDGCGVKYIPN..GPLDK
Retrocopy HVIERLCGAKFKFPGHQKICISKK*GFTK<ENTDRFEDMLAEKQLIPDGCGVKYIPNM<GPLDK

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_1986 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 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004369	2 retrocopies	retro_dord_14, retro_dord_715,
Echinops telfairi	ENSETEG00000001712	10 retrocopies	retro_etel_1073, retro_etel_1284, retro_etel_1517, retro_etel_1654, retro_etel_249, retro_etel_338, retro_etel_403, retro_etel_47, retro_etel_538, retro_etel_631,
Gorilla gorilla	ENSGGOG00000000131	4 retrocopies	retro_ggor_1873, retro_ggor_2425, retro_ggor_253, retro_ggor_61,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Macaca mulatta	ENSMMUG00000005494	5 retrocopies	retro_mmul_1506, retro_mmul_1654, retro_mmul_307, retro_mmul_335, retro_mmul_906,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Tupaia belangeri	ENSTBEG00000003734	1 retrocopy	retro_tbel_61,
Tarsius syrichta	ENSTSYG00000004067	7 retrocopies	retro_tsyr_11, retro_tsyr_1644, retro_tsyr_1739, retro_tsyr_1986 , retro_tsyr_559, retro_tsyr_640, retro_tsyr_960,
Tursiops truncatus	ENSTTRG00000011407	7 retrocopies	retro_ttru_1085, retro_ttru_122, retro_ttru_1226, retro_ttru_1437, retro_ttru_820, retro_ttru_858, retro_ttru_867,