RetrogeneDB ID: retro_tsyr_1186

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_34093:9168..10124(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSTSYG00000007804
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle [Source:HGNC Symbol;Acc:823]

Sequence

>retro_tsyr_1186
GTCTCCAGAAATGCTTTGGGTTCATCGTTCATTGCCACAAGGAACCTCCATGCCTCTAGCACTCGTCTTCAGAAGACTAG
CACTGCTGAGATGTCTATTCTTGAAGAGCGTATTCTCGGAGCTGATACCTCTGTTGACCTTGAGGAGACTGGGCATGTCT
TAAGTATTGGTGATAGTGTTGCTTGAGTTCATAGGCTGAGGAATGTTCAAGCAGAAGAAATGGTAGTATTTTCTTCAGGT
TTACAGGGTATGTCTCTGAACTTGGAACCTGACAACGTCGGGGTTGTCGTATTTGGAAATGATAAGCTGATTAAGGAAGG
AGACATTGTGAAGAGATGGGGAGCCATCGTGGATGCGCCCGTGGGTGAGGAGCTACTGGGCCGGGTGGTGGACGCCCTTG
GTAATGCCATTGTCAGAAAGGGTTCAGTTGGTTCTAAGACCCATAGGCGAGTTTGTCTGAAAGCCCCTGGAATCATTCCT
CGAATCTCAGTACGGGAACCCATGCGGACTGGCATTAAGGCTGTGGATAGCTTGGTGCGAATTGGTCGTGGTCAGCGTGA
GCTGATTATTGATGACAGACAGACTGGGAAAACCTCCATTTCTATCGATACGATCATTAACCAGAAGCGCTTCAATGACG
GAACTGATAAGAAGAAGAAGCTGTACTGCATCTATGTGGCTGTTGGGCAGAAGAGGTCCATGGTGGCCCACCTGGTGAAG
AGGCTCGCAGACGCAGATGCCATGAAGTACACTACCGTGGTGTCAGACACGGCTTCAGATGCTGCCCCACTACAGTACCT
GGCTCCTTACTCTGGCTGTTCCATGGGAGAGTATTTTAGAGACAATGGCAAACATGCTTTGATCATCTATGACGACTTAT
CCAAACAGGCTGTTGCTTACCACCAGATATCTTTGCTTCTCCGCCCCCAGGTGGGGAGGCCTACCCTGGAGAGATG

Alignment

ORF - retro_tsyr_1186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.51 %
• Parental protein coverage: 60.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSRNALGSSFIATRNLHASNTHLQKTGTAEMSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNV
          VSRNALGSSFIATRNLHAS.T.LQKT.TAEMS.ILEERILGADTSVDLEETG.VLSIGD..A.VH.LRNV
Retrocopy VSRNALGSSFIATRNLHASSTRLQKTSTAEMS-ILEERILGADTSVDLEETGHVLSIGDSVA*VHRLRNV

Parental  QAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDG
          QAEEMV.FSSGL.GMSLNLEPDNVGVVVFGNDKLIKEGDIVKR.GAIVD.PVGEELLGRVVDALGNAI..
Retrocopy QAEEMVVFSSGLQGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRWGAIVDAPVGEELLGRVVDALGNAIVR

Parental  KGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQK
          KG..GSKT.RRV.LKAPGIIPRISVREPM.TGIKAVDSLV.IGRGQRELII.DRQTGKTSI.IDTIINQK
Retrocopy KGSVGSKTHRRVCLKAPGIIPRISVREPMRTGIKAVDSLVRIGRGQRELIIDDRQTGKTSISIDTIINQK

Parental  RFNDGTDEKKKLYCIYVAVGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYF
          RFNDGTD.KKKLYCIYVAVGQKRS.VA.LVKRL.DADAMKYT.VVS.TASDAAPLQYLAPYSGCSMGEYF
Retrocopy RFNDGTDKKKKLYCIYVAVGQKRSMVAHLVKRLADADAMKYTTVVSDTASDAAPLQYLAPYSGCSMGEYF

Parental  RDNGKHALIIYDDLSKQAVAYRQMSLLLR-RPPGREAYPGDV
          RDNGKHALIIYDDLSKQAVAY.Q.SLLLR..P.G.EAYPG..
Retrocopy RDNGKHALIIYDDLSKQAVAYHQISLLLR<PPGG-EAYPGEM

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_1186 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 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002507	2 retrocopies	retro_btau_1380, retro_btau_1426,
Canis familiaris	ENSCAFG00000017648	2 retrocopies	retro_cfam_1483, retro_cfam_516,
Dasypus novemcinctus	ENSDNOG00000006331	2 retrocopies	retro_dnov_1740, retro_dnov_2525,
Equus caballus	ENSECAG00000021561	1 retrocopy	retro_ecab_788,
Homo sapiens	ENSG00000152234	1 retrocopy	retro_hsap_1702,
Gorilla gorilla	ENSGGOG00000016560	1 retrocopy	retro_ggor_1275,
Meleagris gallopavo	ENSMGAG00000009963	1 retrocopy	retro_mgal_14,
Microcebus murinus	ENSMICG00000017500	1 retrocopy	retro_mmur_1210,
Myotis lucifugus	ENSMLUG00000009856	1 retrocopy	retro_mluc_1198,
Macaca mulatta	ENSMMUG00000003570	1 retrocopy	retro_mmul_1208,
Mustela putorius furo	ENSMPUG00000000923	1 retrocopy	retro_mputfur_601,
Nomascus leucogenys	ENSNLEG00000010973	1 retrocopy	retro_nleu_1334,
Pongo abelii	ENSPPYG00000009130	1 retrocopy	retro_pabe_1363,
Pan troglodytes	ENSPTRG00000009991	1 retrocopy	retro_ptro_1151,
Sarcophilus harrisii	ENSSHAG00000017177	1 retrocopy	retro_shar_109,
Tarsius syrichta	ENSTSYG00000007804	1 retrocopy	retro_tsyr_1186 ,
Tursiops truncatus	ENSTTRG00000005118	1 retrocopy	retro_ttru_159,