RetrogeneDB ID: retro_tsyr_1659

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_53362:5583..6320(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSTSYG00000004483
• Aliases: None
• Description: citrate synthase [Source:HGNC Symbol;Acc:2422]

Sequence

>retro_tsyr_1659
AATGCATCCTGTCTTATTCTTGCTGTCCAGCTTGCCAGTGCTTCTTCCACAAATTTGAAAGACATATTGGTAGACCTGAT
ACCTGAGGAGCAGACCAGAATTAAGACCTTCAGGCAGCAACATGGTAAGACAGTGGTGGGCCAGATCACTGTGGATATGA
TGTATGGTTGCATGAGAGGCATGAAGGAATTGATATATGAAACATCAGTTCTTGATCCTGATGAAGGCATCCATTTTCAA
GGCTTTAGTATTCCTGAATGCTAGAAACTGCTATCAAGGCTAAAGGTGGGGAAGAACCCCTGCCTGAGGACCTATTTTGG
CTGCTGGTAACAGGACAGTTCCCAAAAGAGGAGCAGATATCTTGACTTTCAAAAGAGTGGGCAAAGAGGGCAGCTCTGTC
TTCCCATGTGATCACCATGCTGGAAAACTTTCCCACCAATCTATACCCCATGCCTCAATTCAGTGCAGCCATTACAGCCC
TCAACAGTGAAAGTAACTTTGCCAGAGCATATGCAGAGGGTATCATCCGAACCAAGTACTAGGAGTTGACTTATGAAGAC
TGTATGGATCTGATTGCAAAACTACATTGTGTTGCAGCAGAAATCTGCCGAAATCTGTACTGGAGGGGCAGCAGTATTGG
GGCCATTGACTCTATACTAGACTAGTCCCACAATTTCACGAACATGTTAGGCTATACTCTTGCTCGGTTCACTGAGCTCA
TGCGTTGGTACCTCACC

Alignment

ORF - retro_tsyr_1659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.81 %
• Parental protein coverage: 54.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NASCLVLAARHASASSTNLKDILAGLIPKEQARIKTFRQQHGKTVVGQITVDMMYGGMRGMKGLVYETSV
          NASCL.LA...ASASSTNLKDIL..LIP.EQ.RIKTFRQQHGKTVVGQITVDMMYG.MRGMK.L.YETSV
Retrocopy NASCLILAVQLASASSTNLKDILVDLIPEEQTRIKTFRQQHGKTVVGQITVDMMYGCMRGMKELIYETSV

Parental  LDPDEGIRFRGFSIPECQKLLP-KAKGGEEPLPEGLFWLLVTGQIPTDEQVSWLSKEWAKRAALPSHVVT
          LDPDEGI.F.GFSIPEC.KLL..KAKGGEEPLPE.LFWLLVTGQ.P..EQ.S.LSKEWAKRAAL.SHV.T
Retrocopy LDPDEGIHFQGFSIPEC*KLLS<KAKGGEEPLPEDLFWLLVTGQFPKEEQIS*LSKEWAKRAALSSHVIT

Parental  MLDNFPTNLHPMSQFSAAITALNSESNFARAYAEGINRTKYWELIYEDCMDLIAKLPCVAAKIYRNLYRE
          ML.NFPTNL.PM.QFSAAITALNSESNFARAYAEGI.RTKY.EL.YEDCMDLIAKL.CVAA.I.RNLY..
Retrocopy MLENFPTNLYPMPQFSAAITALNSESNFARAYAEGIIRTKY*ELTYEDCMDLIAKLHCVAAEICRNLYWR

Parental  GSSIGAIDSKLDWSHNFTNMLGYTDAQFTELMRLYLT
          GSSIGAIDS.LD.SHNFTNMLGYT.A.FTELMR.YLT
Retrocopy GSSIGAIDSILD*SHNFTNMLGYTLARFTELMRWYLT

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_1659 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 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659 ,