RetrogeneDB ID: retro_tsyr_1779

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_582370:1..867(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCLY
• Ensembl ID: ENSTSYG00000002756
• Aliases: None
• Description: selenocysteine lyase [Source:HGNC Symbol;Acc:18161]

Sequence

>retro_tsyr_1779
GCCAAGCCCCATTTTATTACTTGCACAATGGAACACGACTCCATCCGTCTGCCCCTGGAGCACCTGGTGGAGGAACAAGT
GACAGAGGTCACCTTTGTCCTGGTGTCCAGGATGAGCGGGCGGGCAGAGGTGGATAACATCCTTGCGGCCGTCCGCCCAA
CCACACGCCTCGTAACCATCATGCTGGCCAATAATGAGACTGGCATCATCATGCTCATCCCTGAAATCAGTCAGTGTGTT
AAAACCCAAAACCAGAAGCGGGCGGCCACTGGGCTGCCTCCTATCCTGGTGCACACAGATGCTGCACAAGCCTTGGGGAA
AAGGCTTGTGGATGTGGAAGACCTGGGTGTGGACTTCCTTACAATCATGGGGCACAAGTTCTATGGTCCCAGGATTGGTG
CGCTTTATGTAGAGGCCTCAGTGACCTTACTCCTCTGCACCCTATGCTGTTTGGAGGTGGACAAGAATGGAATTTCAGGC
CAGGGACAGAGAACACACCAATGATTGCCGGCCTTGGGAAGGCCGCTGAGCTAGTGACCCAGAACTGTGAAGTGTATGAG
GCCCACATGAGGGACATTTGGGATTAGCTGGAGGAGAGGCTGGAGGCTGAATTTGATGAGAGAATTCATTTGAATAGCCA
GTTTCCAGGGGCTGAATGGCTTCCCAACACTTGCAACTTCTCCATCCAGGGACTCCAACTTCAAGGCCGCCTGGTACTCA
CACAGTGCCAGACACTGATGACCAGTGTAGGGGCTGCATGCCACTCGGACCATGGAGACCAGGCATCCCCAGTGTTGCTG
AGTTGCGGCATCCCCTTCAATGTGACCAGGACGCACTCTGGCTCGTGTGGCCGCAGCACCACCAGG

Alignment

ORF - retro_tsyr_1779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.38 %
• Parental protein coverage: 65.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKPHFITCTVEHDSIRLPLEHLVEEQVAEVTFVPVSRVSGRAEVDDILAAVRPTTRLVTIMLANNETGII
          AKPHFITCT.EHDSIRLPLEHLVEEQV.EVTFV.VSR.SGRAEVD.ILAAVRPTTRLVTIMLANNETGII
Retrocopy AKPHFITCTMEHDSIRLPLEHLVEEQVTEVTFVLVSRMSGRAEVDNILAAVRPTTRLVTIMLANNETGII

Parental  MPIPEISQCVKTQNQKRAATGLPPILMHTDAAQALGKRRVDVEDLGVDFLTIVGHKFYGPRIGALYV-RG
          M.IPEISQCVKTQNQKRAATGLPPIL.HTDAAQALGKR.VDVEDLGVDFLTI.GHKFYGPRIGALYV.RG
Retrocopy MLIPEISQCVKTQNQKRAATGLPPILVHTDAAQALGKRLVDVEDLGVDFLTIMGHKFYGPRIGALYV<RG

Parental  LGDLTPLHPMLFGGGQEWNFRPGTENTPMIAGLGKAAELVTQNCEVYDAHMRDIRDYLEERLEAEFDERI
          L.DLTPLHPMLFGGGQEWNFRPGTENTPMIAGLGKAAELVTQNCEVY.AHMRDI.D.LEERLEAEFDERI
Retrocopy LSDLTPLHPMLFGGGQEWNFRPGTENTPMIAGLGKAAELVTQNCEVYEAHMRDIWD*LEERLEAEFDERI

Parental  HLNSQFPGAERLPNTCNFSIRGPQLQGRLVLTQCRTLMASVGAACHSDHGDR-YPMLLSCGIPFNVTRNT
          HLNSQFPGAE.LPNTCNFSI.G.QLQGRLVLTQC.TLM.SVGAACHSDHGD...P.LLSCGIPFNVTR.T
Retrocopy HLNSQFPGAEWLPNTCNFSIQGLQLQGRLVLTQCQTLMTSVGAACHSDHGDQASPVLLSCGIPFNVTR-T

Parental  LWLSVGRSTTR
          ...S.GRSTTR
Retrocopy HSGSCGRSTTR

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_1779 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013824	2 retrocopies	retro_chof_1528, retro_chof_1707,
Callithrix jacchus	ENSCJAG00000000471	1 retrocopy	retro_cjac_3989,
Oryctolagus cuniculus	ENSOCUG00000002777	1 retrocopy	retro_ocun_405,
Tarsius syrichta	ENSTSYG00000002756	1 retrocopy	retro_tsyr_1779 ,
Tarsius syrichta	ENSTSYG00000005561	1 retrocopy	retro_tsyr_412,