RetrogeneDB ID: retro_tsyr_2106

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_91623:3253..3935(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000009845
• Aliases: None
• Description: None

Sequence

>retro_tsyr_2106
CCAGCACTCGCATTGTAGTCACCAATGGAAATCAAGCAGGAGCCCTAGGATTGATGCATTGATTCAGAAGTATCTAACTG
CTCATCATCCTACATAAGAGGAGGTTACTTCTCTAGCAGCCATGAAGGTTTTTCATATGAAAAATATCCCTAGTTATACT
TTGACGACACTTGTATTGTACCTGAGAGACTGGAAAGCAAAGTCAAACAGGAGCCCACTATGTACCAGGAGGGACTCCCT
TACCAGAGATGAGGTTCCCTTCAGCTGTGGCAGTTCCTGGTCACCCTTTCTGATGACTCAATGGTCACATCATTGCCTGA
ACAGGTGAGACATGGAGTTCAAGCTGCTAAAACCTGAAGAGATTGTTCAACATTGGGGACATACAGAAGAACTAGCCAGC
CATGAACTATGACAAGTTGAGGCATTCTCTACACTGTGTCTATGAAAAAGCTTCACGCAGAAGGTGTCTAGGAAGCAATA
CATCTACAAATTTGTCTGTGACCCAGATGCCCTTTCCTCCATGGCCTTCTCAGACAATCAGCAACTATTCCTGAAGGCAG
AGTCTGAGTGCCACCTTAAGGGAGAAGACACCCTGCCACTGACTCACTTTGAAGACAACCCTGCTTACCTCCTGGACATG
GATCTCTATGGCAGCCTCCCCTATGCTAAAGGCTTTGTTTAC

Alignment

ORF - retro_tsyr_2106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.39 %
• Parental protein coverage: 53.5 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PAHGFQSPMGIKQEPRDYCVDSEVPNCQSSYMRGGYFSSSHEGFSYEKDPRLYFDDTCVVPERLEGKVKQ
          PA....SPM.IKQEP.D.C.DSEV.NC.SSY.RGGYFSSSHEGFSYEK.P.LYFDDTC.VPERLE.KVKQ
Retrocopy PALAL*SPMEIKQEP*D*CIDSEVSNCSSSYIRGGYFSSSHEGFSYEKYP*LYFDDTCIVPERLESKVKQ

Parental  EPTMYREGPPYQRRGSLQLWQFLVTLLDDPA-NAHFIAWTGR-GMEFKLIEPEEVARRWG-IQKNRPAMN
          EPTMY.EG.PYQR.GSLQLWQFLVT.L.D...N.H.IA.TG...MEFKL..PEE....WG.IQKN.PAMN
Retrocopy EPTMYQEGLPYQR*GSLQLWQFLVT-LSDDS<NGHIIA*TGE<DMEFKLLKPEEIVQHWG>IQKN*PAMN

Parental  YDKLSRSLRYYYE-KGIMQKVAGERYVYKFVCDPDALFSMAFPDNQRPYLKAESECHLNEEDTLPLTHFE
          YDKL..SL...YE.K...QKV....Y.YKFVCDPDAL.SMAF.DNQ...LKAESECHL..EDTLPLTHFE
Retrocopy YDKLRHSLHCVYE<KSFTQKVSRKQYIYKFVCDPDALSSMAFSDNQQLFLKAESECHLKGEDTLPLTHFE

Parental  DNPAYLLDMDRCGSLPYAEGFAY
          DNPAYLLDMD..GSLPYA.GF.Y
Retrocopy DNPAYLLDMDLYGSLPYAKGFVY

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_2106 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013420	1 retrocopy	retro_cfam_1414,
Mus musculus	ENSMUSG00000013089	1 retrocopy	retro_mmus_572,
Rattus norvegicus	ENSRNOG00000001785	2 retrocopies	retro_rnor_1500, retro_rnor_417,
Tarsius syrichta	ENSTSYG00000009845	1 retrocopy	retro_tsyr_2106 ,