RetrogeneDB ID: retro_tsyr_415

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_113069:542..1215(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSTSYG00000013466
• Aliases: None
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_tsyr_415
TTGGCTAAGGACATGAAGATCAAGTTGCTGGAGTAGACCTCCCCCTTCTCCTGCCCATCAAGGAGGCTGAGATCACTGAC
TTCTTTCTTGGGGCATCTCTGAAGGATGAGCTTTTTAAAGATTATGCCGGTGCAAAAGCTGGCCCGCGCTGGCCAGTAGT
CCAGGTTCAACGTATTTGTTGCCATCGGGGACTACAGTGACCACGTTGGTCTGGGTGTTAATTATTCCAAGGAGGAAGCC
ACAGCCATCCGAGGGGCCATCATCCTAGCCAAGCTCTCCAGTGTCCCTGTGTGGAGAGGCTGCTGGGGGCACAAGGTTAG
CTAACCCCACACTGTCCCCTGCAAGGTGACCGGCCTCTGTGGCTTTGTGCTGGTGTGCCTTATCCCTGCCCCGAGGGGCA
CTGGCATTGTCTTAGCCCCTATGCCCAAGAAGCTGCTGCTGATGGCCGGTATTGACGACTGCCACCCCTCGGCCAGGGGC
AGCCCTGCCACCCTGAGCAACTTCGCCAAGGCCATCTTTGATGCCGTCTCTAAGACCTTAGCTACTTGACCCCGACTTCT
GGAAAGAGACTGTATTCACCCAGTCTCCCTATCAGGAATTCACTGGCCATCTTGTCAAGACCCACACCAGAGTCTCTGTG
CCAAGGACCCAGGTTCCCACTGTGGCAACAACA

Alignment

ORF - retro_tsyr_415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVKDMKIKSLEENYLFS-LPIKESEIIDFFLGASLKDEV-LKIMPVQKQTRAGQRTRFKAFVAIGDYNGH
          L.KDMKIK.LE....FS.LPIKE.EI.DFFLGASLKDE..LKIMPVQK..RAGQ..RF..FVAIGDY..H
Retrocopy LAKDMKIKLLE*TSPFS<LPIKEAEITDFFLGASLKDEL>LKIMPVQKLARAGQ*SRFNVFVAIGDYSDH

Parental  VGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHNSPCKVTGRCGSVLVRLIPAPRGTGIVS
          VGLGV..SKE.ATAIRGAIILAKLS.VPV.RG.WG.K...PH..PCKVTG.CG.VLV.LIPAPRGTGIV.
Retrocopy VGLGVNYSKEEATAIRGAIILAKLSSVPVWRGCWGHKVS*PHTVPCKVTGLCGFVLVCLIPAPRGTGIVL

Parental  APVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKT-YSYLT-PDLWKETVFTKSPYQEFTDHLV
          AP.PKKLL.MAGIDDC..SARG..ATL.NFAKA.FDA.SKT..SYLT.PD.WKETVFT.SPYQEFT.HLV
Retrocopy APMPKKLLLMAGIDDCHPSARGSPATLSNFAKAIFDAVSKT<LSYLT<PDFWKETVFTQSPYQEFTGHLV

Parental  KTHTRVSMQRTQAPAVSTT
          KTHTRVS..RTQ.P.V.TT
Retrocopy KTHTRVSVPRTQVPTVATT

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_415 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 6 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Felis catus	ENSFCAG00000029191	6 retrocopies	retro_fcat_1245, retro_fcat_1328, retro_fcat_1606, retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tarsius syrichta	ENSTSYG00000013466	52 retrocopies	retro_tsyr_1069, retro_tsyr_1078, retro_tsyr_1147, retro_tsyr_1301, retro_tsyr_131, retro_tsyr_1317, retro_tsyr_1466, retro_tsyr_1478, retro_tsyr_1498, retro_tsyr_1505, retro_tsyr_1509, retro_tsyr_1536, retro_tsyr_1564, retro_tsyr_1568, retro_tsyr_1588, retro_tsyr_1614, retro_tsyr_1636, retro_tsyr_1658, retro_tsyr_169, retro_tsyr_1789, retro_tsyr_1804, retro_tsyr_1827, retro_tsyr_186, retro_tsyr_1929, retro_tsyr_1935, retro_tsyr_2016, retro_tsyr_2175, retro_tsyr_290, retro_tsyr_349, retro_tsyr_415 , retro_tsyr_417, retro_tsyr_463, retro_tsyr_472, retro_tsyr_525, retro_tsyr_527, retro_tsyr_545, retro_tsyr_568, retro_tsyr_604, retro_tsyr_605, retro_tsyr_609, retro_tsyr_61, retro_tsyr_622, retro_tsyr_638, retro_tsyr_650, retro_tsyr_672, retro_tsyr_689, retro_tsyr_691, retro_tsyr_699, retro_tsyr_768, retro_tsyr_773, retro_tsyr_922, retro_tsyr_980,