RetrogeneDB ID: retro_tsyr_1595

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_503294:280..904(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLBP
• Ensembl ID: ENSTSYG00000000376
• Aliases: None
• Description: stem-loop binding protein [Source:HGNC Symbol;Acc:10904]

Sequence

>retro_tsyr_1595
TTTACCACTCCCAAAGGCCCTAAGTCTAGGTCTAGATGTTCAGACTTGGCAAGTAAAGTTGAAGAGGATGAAATGAGGAC
CAAAGGCAACAAAGGGTTGCAAGATACAAAAGAAAACTCCTCATAAATGACTTTGGGAGAAAGAGAAAATCATCATCAGG
AAGTTCTGGCTCAAAGGAGTTTATGTCTATAGTGCCAACTGACTTTGAGACAGATGAAAGTGTCCTGATGAGGAGGCAGA
AGCAGATCAACTATGGGAAGAACACGATTGCCTATGATCGTTATATTAAAGAAGTCCCCAGACACCTTCGACAACCTGGT
ATCCCAAGACCCCCAACAAATTTAAGTATAGTCGACGGTCACAGGACCAGTAATCAAACTCTGGAAGGTGGTTCTTCATT
CTTGGGATCCTCCAACTTAAGAAGGATGTCATTTGAAGGAAATATACCCTGTAGACCTGGAATCCGCAGAAAGCAGCTTT
GAGTTCCAGATGAGCCCTCAGGATGACTTTGATGTATACTCGGGCACAACCCCCAAAGTCAGACATATGGACTGCCAAGT
GGAGGACGGGTTTGATTTGGAAAATTGTTTAATGGAACCCTTGAAAGACTTCTCAGCCATGAGC

Alignment

ORF - retro_tsyr_1595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.24 %
• Parental protein coverage: 78.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FTTPEGPKPRSRCSDWASAVEEDEMRTRVNK-EIARYKRKLLINDFGRERKSSSGSSDSKESMSTVPADF
          FTTP.GPK.RSRCSD.AS.VEEDEMRT..NK...ARYKRKLLINDFGR.RKSSSGSS.SKE.MS.VP.DF
Retrocopy FTTPKGPKSRSRCSDLASKVEEDEMRTKGNK<RVARYKRKLLINDFGRKRKSSSGSSGSKEFMSIVPTDF

Parental  ETDESVLMRRQKQINYGKNTIAYDRYIKEVPRHLRQPGIHPK-TPNKFKKYSRRSWDQ-QIKLWKVALHF
          ETDESVLMRRQKQINYGKNTIAYDRYIKEVPRHLRQPGI.P..TPNKF.KYSRRS.DQ..IKLWKV.LH.
Retrocopy ETDESVLMRRQKQINYGKNTIAYDRYIKEVPRHLRQPGI-PR<TPNKF-KYSRRSQDQ<VIKLWKVVLHS

Parental  WDPPAEEGCDLQEIHPVDLESTESSSEPQTSSQDDFDVYSGTPTKVRHVDCQVEDEFDLETCLMEPLKDF
          WDPP..EGC.L.EI.PVDLES.ESS.E.Q.S.QDDFDVYSGT..KVRH.DCQVED.FDLE.CLMEPLKDF
Retrocopy WDPPT*EGCHLKEIYPVDLESAESSFEFQMSPQDDFDVYSGTTPKVRHMDCQVEDGFDLENCLMEPLKDF

Parental  SAMS
          SAMS
Retrocopy SAMS

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_1595 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001328	1 retrocopy	retro_btau_1456,
Cavia porcellus	ENSCPOG00000000031	1 retrocopy	retro_cpor_364,
Mus musculus	ENSMUSG00000004642	1 retrocopy	retro_mmus_1169,
Otolemur garnettii	ENSOGAG00000009750	1 retrocopy	retro_ogar_1463,
Pteropus vampyrus	ENSPVAG00000002807	2 retrocopies	retro_pvam_490, retro_pvam_941,
Rattus norvegicus	ENSRNOG00000037162	2 retrocopies	retro_rnor_1864, retro_rnor_2016,
Tarsius syrichta	ENSTSYG00000000376	2 retrocopies	retro_tsyr_1595 , retro_tsyr_482,
Tursiops truncatus	ENSTTRG00000010901	1 retrocopy	retro_ttru_10,