RetrogeneDB ID: retro_tsyr_1926

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_67674:985..1560(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGH
• Ensembl ID: ENSTSYG00000008465
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class H [Source:HGNC Symbol;Acc:8964]

Sequence

>retro_tsyr_1926
ATGGAGGGCAAGCGCAGCTTCTCGGATATATGCGGCAACCGCCTGGTCCTACAGTGCCGCTACTACTCCCCGTCGTTGCG
GGAGTTCTGCCTCAGCTGCCCTCGGCTGTCGCTGTGCTCGCTCACCGCTGTCACCTGCAGCGTGTGGCTCGCGGCCTGTG
GGCTCTTCACCCTCTGCGAGAACAGCATGACAGCATGATCCTCTCTGCTGCCATTTTCATCACCCTCTTAGGCCTGCTTG
GGTACCTTCATTTTGTGAAGATTGACCAGGAGACTCTGTTAATCATTGATTCTGTTGGCAACCAGATGACTTCATCCTAT
GCTTCAGGCAAAGAAAGCACTAACTTCATAGAGATGGGCAAGGTCAAGGATGTTGTCATCAATGAGGCTATTTACATGCA
GAAGGTGATTTACTACCTCTGCATCTTACTGAAGGATCCAGTGGAACCACATGGCATATCCCAAGTAGTACCTGTCTTCT
AGAGTGCCAAGCCCCAACTGGACTGCCAGTGTATCGAAGTGTACCGGAGTTGCCAGGAGATCCTGGTGCATCAGCAGAAA
AACGTTGGCATGCCC

Alignment

ORF - retro_tsyr_1926 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGERSFSDVCGGRLVLQCRYYSPSCREFCVSCPRLSLRSVTAVTCSVWLAAYGLFILCENSMILSAAIF
          MEG.RSFSD.CG.RLVLQCRYYSPS.REFC.SCPRLSL.S.TAVTCSVWLAA.GLF.LCENSM.......
Retrocopy MEGKRSFSDICGNRLVLQCRYYSPSLREFCLSCPRLSLCSLTAVTCSVWLAACGLFTLCENSMTA*SSLL

Parental  -ITLLGLLGYL---HFVKIDQETLLIIDSVGIQMTSSYASGKESTNFIEMSKVKDVVINEAIYMQKVIYY
          ......LLG.L...HFVKIDQETLLIIDSVG.QMTSSYASGKESTNFIEM.KVKDVVINEAIYMQKVIYY
Retrocopy <AIFITLLGLLGYLHFVKIDQETLLIIDSVGNQMTSSYASGKESTNFIEMGKVKDVVINEAIYMQKVIYY

Parental  LCILLKDPVEPHGISQVVPVFQSAKPRLDC-LIEVYRSCQEILAHQQAASASP
          LCILLKDPVEPHGISQVVPVF.SAKP.LDC..IEVYRSCQEIL.HQQ.....P
Retrocopy LCILLKDPVEPHGISQVVPVF*SAKPQLDCQCIEVYRSCQEILVHQQKNVGMP

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_1926 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003328	1 retrocopy	retro_cpor_815,
Echinops telfairi	ENSETEG00000008623	1 retrocopy	retro_etel_844,
Homo sapiens	ENSG00000100564	1 retrocopy	retro_hsap_1506,
Gorilla gorilla	ENSGGOG00000001507	1 retrocopy	retro_ggor_1155,
Macropus eugenii	ENSMEUG00000011325	1 retrocopy	retro_meug_2130,
Myotis lucifugus	ENSMLUG00000004467	1 retrocopy	retro_mluc_910,
Nomascus leucogenys	ENSNLEG00000000739	1 retrocopy	retro_nleu_1747,
Pongo abelii	ENSPPYG00000005925	1 retrocopy	retro_pabe_1255,
Pan troglodytes	ENSPTRG00000006466	1 retrocopy	retro_ptro_1020,
Tarsius syrichta	ENSTSYG00000008465	1 retrocopy	retro_tsyr_1926 ,