RetrogeneDB ID: retro_tsyr_526

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_133113:107..1667(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSX2IP
• Ensembl ID: ENSTSYG00000004276
• Aliases: None
• Description: synovial sarcoma, X breakpoint 2 interacting protein [Source:HGNC Symbol;Acc:16509]

Sequence

>retro_tsyr_526
AGAGAATTAAATATAGTAGCTGTTTTAAATTGTATGTATGAGCTACTTATTCTTCAGTGGAAGAACCTTCTAGCTCAGGA
AAATGTGGAAACACAGAATCTGAAACTGGGAAGTGACATGGACCATCTACAGAACTGCTATACAAAACTAAAGGAACAAC
TGGAAACCTCCAGGAGGGAAATGATCGGGCTTCAGGAAAGACACAGACAATGACAATACAAGAACAGGAATTTGCATCAG
CTACTGAAAATTGAAAAAGATGAGGTACAAAAATTGTAAAACATAATTGCCAGTCAGGCTACTCAGTATAATCATGATAT
GAAGAGAAAAGAGCGTGAATATAATAAACTGAAAGAGCGTCTGCATCAGCTTGTTATGAACATGAAAGATAAAAATATAG
CCATGGACGTTTTGAATTATGTGGGGAGAGCTGATGGCAAGAGAGGCTTCTGGAAGACTGGTAAAATGGAAGCCAGGAAT
GAAGATGAAATGTATAAAATTCTCTTGAATGATTATGAATGCCGTCAGAAACAAATCCTAATGGAAAATGTTGAACTTAA
GAAGGTTCTTCAGCAAATGAAAAAGGAAATGATTTCTCTTCTTTCTTCCCAAAATAAGAAACCCAGAGAAAGAGCGGATG
ATAGTATGGGAACTGTTATCTCTGATGTTCAAGAAGATGCTGGGGAACTGAGCAGAGAGAATATGTGGGACCTTTCCTGT
GAAACTGTGAGAGAGCAGCTCACAAACAGCATCAGAACACAGTGGAGGATTTTGAAAAGTCATGTAGAAAAGTTTGACAA
CCAAGTTTCAAAGATACACTTAGAAGGTTTTAATGATGAAGATGTAATCTCACAAGACCATGAACAAGAAACCGAAAAAC
TTGAGTTAGAAATTCAGCAATGTAAAGAAATGATTAAAACTCAGCAGCAACTTTTACAGCAGCAGCTTGCTACTGCATGT
GATGATGATACCACTTCACTATTACGAGACTGTTATTTCTTGGAAGAAAAGGAATGCCTCAAAGAAGAATGGTCCCTTTT
TAAAGAGCAAAAAAGGAATTTTGAGAGAGAAAGACGAAGCTTTACAGAGGCTGCTATTCGCCTAGGGTTGGAGAGAAAGG
CATTTGAAGAAGAAAGAGACAGTTGGTTAAAGCAACTGTTTTTAAATATGACTACCTTTGACCACCAGAACTCAGAAAAT
GTGAAAATTTTCAGTGCTTTGTCAGGAAGTTCTGATCGGGAAAATCTTATAGTGCACTTGAGGCAACGGCAGAAGAAGCC
TGACGGTGTGTCCAGTGGGTTTCCAGTTTGTACATCTAAACTTACTAAATCTCTTCCGGCTTCACCTTCTACTTCAGAGT
TTTGCCAACCACGTTCCTGTGTATCTGAACATAGGTCAGTCAATGTACTAAATATAACTCCTGAAGAAACCAAACCAAAT
CAGGTTGAAAGAGAATGTACCAATCAGAAGTGGAGCACGGTGTCAAGACCTGGCTCGCAGAATGGCTGCTATGGTGGATG
CTCCTTGAGCTACACAAACTTTTACGTCAAGAAAGATGAC

Alignment

ORF - retro_tsyr_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.6 %
• Parental protein coverage: 84.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RELNIVAVLNCMYELLVLQRKNLLAQENVETQNLKLGSDMDHLQNCYTKLKEQLETSRREMIGLQERDRQ
          RELNIVAVLNCMYELL.LQ.KNLLAQENVETQNLKLGSDMDHLQNCYTKLKEQLETSRREMIGLQER.RQ
Retrocopy RELNIVAVLNCMYELLILQWKNLLAQENVETQNLKLGSDMDHLQNCYTKLKEQLETSRREMIGLQERHRQ

Parental  LQCKNRSLHQLLKNEKDEVQKLQNIIASRATQYNHDMKRKEREYNKLKERLHQLVMNKKDKKIAMEVLNY
          .Q.KNR.LHQLLK.EKDEVQKL.NIIAS.ATQYNHDMKRKEREYNKLKERLHQLVMN.KDK.IAM.VLNY
Retrocopy *QYKNRNLHQLLKIEKDEVQKL*NIIASQATQYNHDMKRKEREYNKLKERLHQLVMNMKDKNIAMDVLNY

Parental  VGRADGKRGSWRTGKTEARNEDEMYKILLNDYEYRQKQILMENAELKKVLQQMKKEMISLLSPQKKKPRE
          VGRADGKRG.W.TGK.EARNEDEMYKILLNDYE.RQKQILMEN.ELKKVLQQMKKEMISLLS.Q.KKPRE
Retrocopy VGRADGKRGFWKTGKMEARNEDEMYKILLNDYECRQKQILMENVELKKVLQQMKKEMISLLSSQNKKPRE

Parental  RADDSTGTAISDVEEDAGELSRENMWDLSCETVREQLTNSIRTQWRILKSHVEKLDNQVSKVHLEGFNDE
          RADDS.GT.ISDV.EDAGELSRENMWDLSCETVREQLTNSIRTQWRILKSHVEK.DNQVSK.HLEGFNDE
Retrocopy RADDSMGTVISDVQEDAGELSRENMWDLSCETVREQLTNSIRTQWRILKSHVEKFDNQVSKIHLEGFNDE

Parental  DVISRQDHEQETEKLELEIQQCKEMIKTQQQLLQQQLATACDDDTTSLLRDCYLLEEKERLKEEWSLFKE
          DVIS.QDHEQETEKLELEIQQCKEMIKTQQQLLQQQLATACDDDTTSLLRDCY.LEEKE.LKEEWSLFKE
Retrocopy DVIS-QDHEQETEKLELEIQQCKEMIKTQQQLLQQQLATACDDDTTSLLRDCYFLEEKECLKEEWSLFKE

Parental  QKKNFERERRSFTEAAIRLGLERKAFEEERASWLKQQFLNMTTFDHQNSENVKLFSAFSGSSDRDNLIAH
          QK.NFERERRSFTEAAIRLGLERKAFEEER.SWLKQ.FLNMTTFDHQNSENVK.FSA.SGSSDR.NLI.H
Retrocopy QKRNFERERRSFTEAAIRLGLERKAFEEERDSWLKQLFLNMTTFDHQNSENVKIFSALSGSSDRENLIVH

Parental  SRQRQKKPHGVSSGSPVCTSKLTKSLPASPSTSDFCQPRSCVSEHSSVNILNISPEETKPNQVRRECTNQ
          .RQRQKKP.GVSSG.PVCTSKLTKSLPASPSTS.FCQPRSCVSEH.SVN.LNI.PEETKPNQV.RECTNQ
Retrocopy LRQRQKKPDGVSSGFPVCTSKLTKSLPASPSTSEFCQPRSCVSEHRSVNVLNITPEETKPNQVERECTNQ

Parental  RWSVVSRPGLQEGCYGGCSLTYTNFHVEKDD
          .WS.VSRPG.Q.GCYGGCSL.YTNF.V.KDD
Retrocopy KWSTVSRPGSQNGCYGGCSLSYTNFYVKKDD

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_526 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000117155	1 retrocopy	retro_hsap_2822,
Pongo abelii	ENSPPYG00000001201	1 retrocopy	retro_pabe_2206,
Pan troglodytes	ENSPTRG00000000906	1 retrocopy	retro_ptro_1913,
Tarsius syrichta	ENSTSYG00000004276	1 retrocopy	retro_tsyr_526 ,
Tursiops truncatus	ENSTTRG00000008402	1 retrocopy	retro_ttru_1078,