RetrogeneDB ID: retro_tsyr_1980

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_74635:2984..3558(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBX1
• Ensembl ID: ENSTSYG00000012332
• Aliases: None
• Description: pre-B-cell leukemia homeobox 1 [Source:HGNC Symbol;Acc:8632]

Sequence

>retro_tsyr_1980
AAACAAGCCCAAAACTGCCACCGAATGAAGACTGTTCTCTTTAATGTCCTGTGTGAAATCAAGGAGAAAGCCGGCCTCAG
CATTCCAAGCTCCCAAGAGGAGGAGACGGTGGACACACAGCTGATGCCCTTGGACATCATGCTTCTGGCAGAGGTTGTGG
CTGGGCCTGAGAAGAGGGGGGGATAGGGATTACTCAGCAGCAGCAGCTGTAGCCGCTGCAGCCTCCAGAGGTGGAGTGTC
CCTTAACAACTCCATGGAACACTCAGACTATGGTAGCAAACTTGCCCAGATCTGCCACATCTTCCACGCGGAACTGGAGA
AGTATGAACAGGCATGTAATGAGCTCACGGCCCGTGTCATGAACCTACTGAGGGAGCAAAGCTACACAAGGCCTGTCACA
CCCAAGGAGATGGAGCGTATTGGAAGCATCATCCATTGAAAGTCCAGTGCCATCCAGATGCAGCTCAAGCAGAGCACCTG
CGAGGACATCGTGGTCCTGCGTTCTCGTTTCCTGAATGCCAGATGAAAACACCGTAACTTCAGCAAACAAGCCAGTGAGG
TCCTGAATGAATAT

Alignment

ORF - retro_tsyr_1980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.75 %
• Parental protein coverage: 51.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KHALNCHRMKPALFNVLCEIKEKTVLSIRGAQEEEPTDPQLMRLDNMLLAEGVAGPE-KGG----GSAAA
          K.A.NCHRMK..LFNVLCEIKEK..LSI...QEEE..D.QLM.LD.MLLAE.VAGPE..GG......AAA
Retrocopy KQAQNCHRMKTVLFNVLCEIKEKAGLSIPSSQEEETVDTQLMPLDIMLLAEVVAGPE>RGGDRDYSAAAA

Parental  AAAAAASGGAGSDNSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIER
          .AAAA..GG....NS.EHSDY..KL.QI..I.H.ELEKYEQACNE.T..VMNLLREQS.TRP..PKE.ER
Retrocopy VAAAASRGGVSLNNSMEHSDYGSKLAQICHIFHAELEKYEQACNELTARVMNLLREQSYTRPVTPKEMER

Parental  MVSIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEY
          ..SIIH.K.S.IQMQLKQSTCE....LRSRFL.AR.K.RNF.KQA.E.LNEY
Retrocopy IGSIIH*KSSAIQMQLKQSTCEDIVVLRSRFLNAR*KHRNFSKQASEVLNEY

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_1980 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001238	1 retrocopy	retro_mdom_1605,
Procavia capensis	ENSPCAG00000002628	1 retrocopy	retro_pcap_310,
Sarcophilus harrisii	ENSSHAG00000012750	1 retrocopy	retro_shar_377,
Tarsius syrichta	ENSTSYG00000012332	3 retrocopies	retro_tsyr_1980 , retro_tsyr_479, retro_tsyr_723,