RetrogeneDB ID: retro_tsyr_1684

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_542286:0..509(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD10
• Ensembl ID: ENSTSYG00000009920
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 10 [Source:HGNC Symbol;Acc:9555]

Sequence

>retro_tsyr_1684
GAATCTTTGTTGCAGCCTTGGAGTGCTAGTGAATTATAAAAACGATGCAGCTTTGTCTGCTCTTCATATTGCTATTTCTG
CTGGCTGGGATGAGATAGTAAAAGCCCTTCTGGGAAAAGGTGCTCAAGTGAATGCTGTCAGTCAAAACGGCTGTACTCCC
CTGCATAATGTGGCTTCCAAAAATAGACAGGGAATTACTGTCTTGTTACTAGAGGGTGGGGCTAATCCAGATGCTAAAAA
CCATTATGAGGGTACAGCCGTCAACCTGGTAGCAGCCAAGGGTAACCTGAAGATGATTCATATCCCTCTGTACTATAAAA
GCATCCACAAACATCCAAGGCATCGAGGGCAGCGCTCCTCTATACTAGTCTGTGATGAGTAGAGGGTGGAAGAAGCAAAA
CTGTTGGTGACCCTCTAGTAACAAGGAGCAAGCATTTATACTGAGAATAAAGAAGAAAAGACCTCTGCAAGTGGCCAAAG
GTGGCCTGGGTCTAATACTCAAGAGAATG

Alignment

ORF - retro_tsyr_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.57 %
• Parental protein coverage: 73.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EFLLQ-LGVPVNDKDDAGWSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVML
          E.LLQ.LGV.VN.K.DA..S.LHIA.SAG.DEIVKALLGKGAQVNAV.QNGCTPLH..ASKNR..I.V.L
Retrocopy ESLLQ>LGVLVNYKNDAALSALHIAISAGWDEIVKALLGKGAQVNAVSQNGCTPLHNVASKNRQGITVLL

Parental  LEGGANPDAKDHYEATAMHRAAAKGNLKMIHILLYY-KASTNIQDTEGNTPLH-LACDEERVEEAKLLVS
          LEGGANPDAK.HYE.TA....AAKGNLKMIHI.LYY.KASTNIQ..EG..PL..L.CDE.RVEEAKLLV.
Retrocopy LEGGANPDAKNHYEGTAVNLVAAKGNLKMIHIPLYY>KASTNIQGIEGSAPLY<LVCDE*RVEEAKLLVT

Parental  ---QGASIDIEN-EGKTSL-VAKGGLGLIPKRM
          ...QGASI..EN.E.KTS..VAKGGLGLI.KRM
Retrocopy L**QGASIYTENKEEKTSA>VAKGGLGLILKRM

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_1684 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 16 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012006	1 retrocopy	retro_acar_134,
Callithrix jacchus	ENSCJAG00000007717	1 retrocopy	retro_cjac_2515,
Cavia porcellus	ENSCPOG00000015068	1 retrocopy	retro_cpor_358,
Dasypus novemcinctus	ENSDNOG00000001902	5 retrocopies	retro_dnov_1194, retro_dnov_208, retro_dnov_705, retro_dnov_824, retro_dnov_835,
Homo sapiens	ENSG00000101843	3 retrocopies	retro_hsap_1214, retro_hsap_2435, retro_hsap_2737,
Gorilla gorilla	ENSGGOG00000002969	3 retrocopies	retro_ggor_1515, retro_ggor_1906, retro_ggor_945,
Macaca mulatta	ENSMMUG00000016981	1 retrocopy	retro_mmul_1290,
Nomascus leucogenys	ENSNLEG00000014001	2 retrocopies	retro_nleu_243, retro_nleu_690,
Oryctolagus cuniculus	ENSOCUG00000010837	1 retrocopy	retro_ocun_793,
Otolemur garnettii	ENSOGAG00000006419	1 retrocopy	retro_ogar_213,
Procavia capensis	ENSPCAG00000005221	1 retrocopy	retro_pcap_461,
Pongo abelii	ENSPPYG00000020618	3 retrocopies	retro_pabe_1010, retro_pabe_1793, retro_pabe_2275,
Pan troglodytes	ENSPTRG00000022169	3 retrocopies	retro_ptro_1407, retro_ptro_1851, retro_ptro_831,
Ictidomys tridecemlineatus	ENSSTOG00000003783	3 retrocopies	retro_itri_1684, retro_itri_312, retro_itri_676,
Tarsius syrichta	ENSTSYG00000000542	1 retrocopy	retro_tsyr_1119,
Tarsius syrichta	ENSTSYG00000009920	13 retrocopies	retro_tsyr_1160, retro_tsyr_1674, retro_tsyr_1684 , retro_tsyr_1741, retro_tsyr_1830, retro_tsyr_1968, retro_tsyr_1989, retro_tsyr_2010, retro_tsyr_2138, retro_tsyr_2151, retro_tsyr_2167, retro_tsyr_674, retro_tsyr_803,