RetrogeneDB ID: retro_tsyr_1649

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_531410:35..880(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSTSYG00000012788
• Aliases: None
• Description: male-specific lethal 3 homolog (Drosophila) [Source:HGNC Symbol;Acc:7370]

Sequence

>retro_tsyr_1649
GACTCAGAGCCGCAAACCCCCAGGGAGATGGAAGGAAGGGCCCTAACAATAGACCTCCCTGAGGTTCTGAAGCAGCAGCT
GGAGGACGATCGCTACTATATTAACAGGAGGAAACGGTTCGTGCAGCTTCCTTGCCAGCCCAACGTCGTCGCCATTTTGG
AGTCCTACCTGAGGCATTTTGCTGGGCACGCTGCCCTTTCGGCCAGGGAGAGGCCTCGCCCCCAGCTCGCCAGGCCGCAG
GCCCACCCCCCGGCGCCTTCCGTGCCTGCCGAAGCGAGTGCTGACCTTTGTAAGGAGATGGCGGATGGCTTGAGGATAAC
CTTTGACTACACTCTCCGGTCGGCTTTGCTCTATCCACACGAACGGGCTCAGTATAAGAAGGTGACGTCCTCTGGGTTTT
CTCTGCCAGGGACGGACAGGACCCCAGACGCTGGCGGGCGCCAGGAGGCTCGCTCTCCCAGCCGGCCTCTGCTGACTCAG
CCCGCGGCGCAGACCCCAGAGGGTCCACCGGGCCCGGGGGACCTCGCCACCCCCAGAAGGCACAGAGCCCAGCCGGCAGC
CTGGCAGGCGCCGAGACGGTCCACGCGCCACGCCGCCCACGCGGCCAGGCTCTCCCAGAGCCGCGCCTCGCCCGGGCCTG
AGCCCCGACAGCAGGACCCGGCCCCCGGCAGGCCCACGCCGTTCCTGCCGCTGGAGACGAGGACGCCCGTGCGCGGCGGA
TGGTCTCCACCTGTCCTGCTGGCGCCCAGCCACGAAGGGAGGGCGGCGTCTGCGGGGTTTGGGGGGAGAAGAACGAATGA
AATGAGGGAGGTTCTCTCCTGTAACTGGTGCCTGAGCATTATCCC

Alignment

ORF - retro_tsyr_1649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.77 %
• Parental protein coverage: 57.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPELQTKREMEERTITIEIPEVLKKQLEDDCYYINRRKRLVKLPCQTNIITILESYVKHFAINAAFSANE
          ..E.QT.REME.R..TI..PEVLK.QLEDD.YYINRRKR.V.LPCQ.N...ILESY..HFA..AA.SA.E
Retrocopy DSEPQTPREMEGRALTIDLPEVLKQQLEDDRYYINRRKRFVQLPCQPNVVAILESYLRHFAGHAALSARE

Parental  RPRHHHAMAHANMNVHYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQTQYKKVTSSKFFLPIKES
          RPR...A...A.......PAE...DLCKEM.DGLRITFDYTL...LLYP.E..QYKKVTSS.F.LP....
Retrocopy RPRPQLARPQAHPPAPSVPAEASADLCKEMADGLRITFDYTLRSALLYPHERAQYKKVTSSGFSLPGTDR

Parental  ATNTSRSXXXXXXNSPLLNPSTPQSTESQPASGEPATPKRRKAEPEALQSLRRSTRHTTNCDRLSESSAS
          ...............PLL.....Q..E..P..G..ATP.R..A.P.A.Q..RRSTRH.....RLS.S.AS
Retrocopy TPDAGGRQEARSPSRPLLTQPAAQTPEGPPGPGDLATPRRHRAQPAAWQAPRRSTRHAAHAARLSQSRAS

Parental  PQPKRRQQDTSASMPKLFLHLEKKTPVHSRSSSPIPLTPSKEGSAVFAGFEGRRTNEINEVLSWK-LVPD
          P.P..RQQD.....P..FL.LE..TPV....S.P..L.PS.EG.A..AGF.GRRTNE..EVLS...LVP.
Retrocopy PGPEPRQQDPAPGRPTPFLPLETRTPVRGGWSPPVLLAPSHEGRAASAGFGGRRTNEMREVLSCN<LVPE

Parental  NYP
          .YP
Retrocopy HYP

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_1649 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009278	1 retrocopy	retro_btau_883,
Callithrix jacchus	ENSCJAG00000001061	1 retrocopy	retro_cjac_1490,
Cavia porcellus	ENSCPOG00000004692	5 retrocopies	retro_cpor_1423, retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens	ENSG00000005302	2 retrocopies	retro_hsap_2401, retro_hsap_4097,
Gorilla gorilla	ENSGGOG00000006582	2 retrocopies	retro_ggor_1820, retro_ggor_2749,
Macaca mulatta	ENSMMUG00000002689	2 retrocopies	retro_mmul_2362, retro_mmul_972,
Monodelphis domestica	ENSMODG00000017350	1 retrocopy	retro_mdom_1422,
Pongo abelii	ENSPPYG00000020123	2 retrocopies	retro_pabe_2166, retro_pabe_3353,
Pan troglodytes	ENSPTRG00000021662	2 retrocopies	retro_ptro_1751, retro_ptro_2778,
Pteropus vampyrus	ENSPVAG00000005000	1 retrocopy	retro_pvam_203,
Sorex araneus	ENSSARG00000008477	1 retrocopy	retro_sara_139,
Tarsius syrichta	ENSTSYG00000012788	4 retrocopies	retro_tsyr_1079, retro_tsyr_1649 , retro_tsyr_1706, retro_tsyr_948,