RetrogeneDB ID: retro_tsyr_717

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_180670:2425..3173(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM183A
• Ensembl ID: ENSTSYG00000007009
• Aliases: None
• Description: transmembrane protein 183A [Source:HGNC Symbol;Acc:20173]

Sequence

>retro_tsyr_717
GAACTGGATGGGGCTGAAGAAGACGAGTAGCCCATGGATATTTACCTATTGTTGGCTTCCTACAACCACCCTGAGGACAT
TGTGAATTTTTCCCTGACTTGTAAGAATGCCTGGACTGTCACTTGCACTGCTGCCTTTTGGACCAGGTTGTACCGAAGAC
ACAACATGCTGGACTCTCCTCTGCCTTTGTTCCTGCAACCAGAGTCAATGGATAATCTGCGATGCCTCTGGGCATGTGTG
ATCCGATCTCTGTACCATATCTATGTGCCAAGGGCTGTTCCAATCTCCAAGAACTCAGCCATTCCAGAAAGCACTCCCAA
CACATTAAAGAATTCCAAATGCTTACTTTTCTGGTGCAGAAAGATTGTTGGGAACAGACAGGAACCAATGTGGGAATCAA
CTTCAAGTTCAAAAACAGTCCCCTAGGTTAAAGAGCAAGTGTACTGGAGGATTACAGTCTCCTGTTCAAAATGGAGATGT
TCATACCAATCCAGACCAGGACTGCCTGCAGGTCACCACCATCAATTTCATCTTTATTCCAGCTGTCATTGAAATGATAT
TTACCCTGTTTGCTACCAACGTGAACACAAATATGTGGCATCATCGAGTGAGACTGGTGTTCCAGGATTCTTCTGTCCAT
GGTGGTTGGAAACTGTGCAGTGAACAGGGTGTGAAAGTTATCCTGGACCCAGTGCACAGCGTTCAACTCTATGACTGGTG
GCATTCTCAGTATCCATTCTCCTTGAGA

Alignment

ORF - retro_tsyr_717 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.71 %
• Parental protein coverage: 67.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELDGAGGEEYPMDIWLLLASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESM
          ELDGA...E.PMDI.LLLASY..PEDIVNFSL.CKNAWTVTCTAAFWTRLYRRH..LD..LPL.L.PESM
Retrocopy ELDGAEEDE*PMDIYLLLASYNHPEDIVNFSLTCKNAWTVTCTAAFWTRLYRRHNMLDSPLPLFLQPESM

Parental  EKLRCLRACVIRSLYHMYEPFAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWE-FNFKFK-
          ..LRCL.ACVIRSLYH.Y.P.A..ISKN.AIPESTP.TLKNSKCLLFWCRKIVGNRQEPMWE..NFKFK.
Retrocopy DNLRCLWACVIRSLYHIYVPRAVPISKNSAIPESTPNTLKNSKCLLFWCRKIVGNRQEPMWE<INFKFK<

Parental  KQSPRLKSKCMGGLQPPVQYEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMRHHRVRL
          KQSPRLKSKC.GGLQ.PVQ..DVHTNPDQDC..LQVTT.NFIFIP.V..MIFTLF..NV.T.M.HHRVRL
Retrocopy KQSPRLKSKCTGGLQSPVQNGDVHTNPDQDC--LQVTTINFIFIPAVIEMIFTLFATNVNTNMWHHRVRL

Parental  VFQDSPVHGGRKLRSEQGVQVILDPVHSVRLFDWWHPQYPFSLR
          VFQDS.VHGG.KL.SEQGV.VILDPVHSV.L.DWWH.QYPFSLR
Retrocopy VFQDSSVHGGWKLCSEQGVKVILDPVHSVQLYDWWHSQYPFSLR

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_717 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 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808, retro_hsap_2863, retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717 ,