RetrogeneDB ID: retro_tsyr_1056

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_290985:389..919(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM1
• Ensembl ID: ENSTSYG00000000834
• Aliases: None
• Description: PDZ and LIM domain 1 [Source:HGNC Symbol;Acc:2067]

Sequence

>retro_tsyr_1056
GTCACTCCTAGAAGCAAGGCCGCTATAGTTAATTTATGTATCAGAGATGTGATCACAGCCATCGATGGAAAAAATACCAA
CAGTATGATGCACTTGGAAGTTCAGAACAAAATCAAGGGCTGCACATACAACATGACATTCACAGTGGCCAGATATGAAC
CTAAAGTCTGGTCTCCTCTGGTGACAAAGGAAGGAAAACATCACAATTCAAGATACATTTAGCCTCCAAACCAGAAGAGG
TCCTGCACATAGGACCATAACCATAACCATAATCAAATTGCCATGTCATTTATCCCCTCATCTGCCTCCAGCACTGCCCC
CGGGGTCATCACGAATCAGTACAATCCACCCGGCCTCTACTCTTCTGAAAACATCTCCAGCTTCAACAACTCTTTCGAGT
CAAAGACTGCTGCCAGAGGGGCGGATGTGAACAGCAGGCCTTTAGACCATGCTCAGCCTCCAAGAGGCCTTGTCATTGAC
AAAGAATCAGAAGTTTACAAGATGCTTCAGAGAAGCAGGAGTTGAATGAG

Alignment

ORF - retro_tsyr_1056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.72 %
• Parental protein coverage: 89.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ITPGSKAAIANLCIGDVITAIDGENTGSMTHLEAQNKIKGCTDNMTLTVARSEHKVWSPLVTEEGKRH-P
          .TP.SKAAI.NLCI.DVITAIDG.NT.SM.HLE.QNKIKGCT.NMT.TVAR.E.KVWSPLVT.EGK.H..
Retrocopy VTPRSKAAIVNLCIRDVITAIDGKNTNSMMHLEVQNKIKGCTYNMTFTVARYEPKVWSPLVTKEGKHH<Q

Parental  YKMNLASEPQEVLHIG-SAHNRS--AMPFTASPASSAAPRVITNQYNNPAGLYSSENISSFNNALESKTA
          .K..LAS.P.EVLHIG...HN....AM.F..S.ASS.AP.VITNQY.NP.GLYSSENISSFNN..ESKTA
Retrocopy FKIHLASKPEEVLHIG>HNHNHNQIAMSFIPSSASSTAPGVITNQY-NPPGLYSSENISSFNNSFESKTA

Parental  ASGEEVNSRPLKHSS-SSSLVLGKELEVYKMLQ-EKQLLNE
          A.G..VNSRPL.H......LV..KE.EVYKMLQ.EKQ.LNE
Retrocopy ARGADVNSRPLDHAQPPRGLVIDKESEVYKMLQ<EKQELNE

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_1056 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056 , retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,