RetrogeneDB ID: retro_tsyr_1815

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_602045:4..733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN28B
• Ensembl ID: ENSTSYG00000006480
• Aliases: None
• Description: lin-28 homolog B (C. elegans) [Source:HGNC Symbol;Acc:32207]

Sequence

>retro_tsyr_1815
CAAGGTGGTGGCGAGGAGCCCCGGGAGCTGCCGGAGCCGGCCCAGGAGGACTCTCTGGTTTTGCATGGAACCCGCCACTG
CAAGTAGTGCAATGTGCGCATGGGATTTGGATTCATCTCCATGATAAGCTGAGAGGAAAGTCCCTTGAATATTCCAGTCG
ATGTATTTGTACACCAAAGCAAACTATTCATGGAAGGATTTAGAAGCCTAAAAGAAGGAGAACCAGTGGAATTCACATTT
AAAAAATCTTCCAAAGGCCTTGAATCAATACGAGTAACAGGACCTGGTGGGAACCCCTGTTTAGGAAGCGAAAGAAGACC
CAAAGGGAAGTCACTACAAAAGAGAAAAGCAAAGGGAGGTAGATGCTACAGCTGTGGTGGCCTTGATCATCATGCTAAGG
AATGTAGTCTACCTCCTCAGCCAGAGAAGTGCCATTACTGTCACAGCATCATGCACATGGCGGCAAACCGCCCACATAAA
ACTGTTGCACAGCCACCCGCCAGTTCTCAGGGAAGACAGGAAGCAGAATTCCAGCCATGCACTTCGGCCTGCCCTCGAGA
GGTGGGAGGTAGGCACGGCTGTCCATCACCCCAGTTTCCTCAGGAGGCAAAGGTGGAGATCTCAGATCGGTCAGGCAGGT
CGCCTCAAGAAGCTTCCTCCATGAAGTCATCTGCAACACCAGAAGAGCAGAGTAAAAAGGGGTCTTCAGTACAAAAAAGG
AAAAAGACA

Alignment

ORF - retro_tsyr_1815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.12 %
• Parental protein coverage: 88.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGGGEEPGKLPEPAEEDSPVLHGTGHCKWFNVRMGFGFISMISREGSPLDIPVDVFVHQSKLFMEGFRSL
          .GGGEEP..LPEPA.EDS.VLHGT.HCK..NVRMGFGFISMIS.E.SPL.IPVDVFVHQSKLFMEGFRSL
Retrocopy QGGGEEPRELPEPAQEDSLVLHGTRHCK*CNVRMGFGFISMIS*EESPLNIPVDVFVHQSKLFMEGFRSL

Parental  KEGEPVEFTFKKSSKGLESIRVTGPGGNPCLGSERRPKGKTLQKRKPKGDRCYNCGGLDHHAKECSLPPQ
          KEGEPVEFTFKKSSKGLESIRVTGPGGNPCLGSERRPKGK.LQKRK.KG.RCY.CGGLDHHAKECSLPPQ
Retrocopy KEGEPVEFTFKKSSKGLESIRVTGPGGNPCLGSERRPKGKSLQKRKAKGGRCYSCGGLDHHAKECSLPPQ

Parental  PKKCHYCQSIMHMVANCPHKTVAQPPASSQGRQEAESQPCTSACPREVGGGHGCPSPQFPQEAKAEISDR
          P.KCHYC.SIMHM.AN.PHKTVAQPPASSQGRQEAE.QPCTSACPREVGG.HGCPSPQFPQEAK.EISDR
Retrocopy PEKCHYCHSIMHMAANRPHKTVAQPPASSQGRQEAEFQPCTSACPREVGGRHGCPSPQFPQEAKVEISDR

Parental  SGRSPQEASSMKSSAAPEEQSKKGPSVQKRKKT
          SGRSPQEASSMKSSA.PEEQSKKG.SVQKRKKT
Retrocopy SGRSPQEASSMKSSATPEEQSKKGSSVQKRKKT

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_1815 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015340	1 retrocopy	retro_etel_1927,
Microcebus murinus	ENSMICG00000002297	4 retrocopies	retro_mmur_1377, retro_mmur_1390, retro_mmur_660, retro_mmur_800,
Oryctolagus cuniculus	ENSOCUG00000017850	1 retrocopy	retro_ocun_532,
Otolemur garnettii	ENSOGAG00000011042	1 retrocopy	retro_ogar_645,
Sorex araneus	ENSSARG00000008374	2 retrocopies	retro_sara_121, retro_sara_746,
Tarsius syrichta	ENSTSYG00000006480	1 retrocopy	retro_tsyr_1815 ,