RetrogeneDB ID: retro_tsyr_267

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_6726:16229..17402(-)
• Located in intron of: ENSTSYG00000003930

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP43
• Ensembl ID: ENSTSYG00000000944
• Aliases: None
• Description: nucleoporin 43kDa [Source:HGNC Symbol;Acc:21182]

Sequence

>retro_tsyr_267
GTTCTTACTCTACCTCCTGCAGTTGCTTTGGGCATGGAGGAAATTTATGCAAAGTTTGTGTCTCAGAAAATCAGCAAAAC
CCGCTGGCGACCGGTGCCCTCAGGGAGCCTACAGACCGCGGAGACGTTCGCTACAGGTTCTTGGGACAATGAGGAAAACT
ATGTTTCGCTGTGGTCTATTGGAGATTTTGGAAACTTGGACTCTGATGGAGGATTTGAAGGAGACCATCAATTATTGTGT
GATATCAGACACCATGGTGATGTAATGGATTTACAGTTTTTTGACCAAGAAAGGATTGTAGCTGCTTCATCAACAGGAAG
CGTAACAGTTTTTCTTCACCATCCGAATAACCAGACTTTGTCAGTCAACCAGCAGTGGACAGCAGCTCACTACCACACAG
GTCCAGGCAGTCCTTCCTATAGCAGTGCACCATGCACAGGTATTGTATGCAGCAACCCAGAAATTGTCACTGTTGGAGAA
GATGGTCGAATAAATTTCTTCAGAGCAGATCACAAGGAAGCTCTAAGAACTATAGACAATGCAGATAGCAGTACACTCCA
TGCTGTAACCTTCCTTCGAACTCCTGAGATTCTTACAGTAAATTCAATTGGACAGTTAAAAATATGGGATTTCAGACAAC
AAGGAAATGAGCCTTCTCAGATATTGTCACTGACTGGTGATCGAGTGCCACTTCACTGTGTTGATAGACATCCTAACCAA
CAGCATGTTGTAGCTACCGGTGGCCAGGATGGAATGTTGAGTATTTGGGATGTTAGACAAGGTACTATGCCTGTATCTCT
GCTGAAGGCTCATGAAGCTGAAATGTGGGAAGTTCACTTTCACCCATCCAACCCAGATCATCTCTTTACTTGTTCTGAAG
ATGGATCCCTCTGGCACTGGGATGCCTCCACAGATGTACCTGAAAAGTCATCACTGTTTCACCAAGGAGGAAGAACTAGC
ACTTTTTTGTCTCATAGCATTAGTAACCAAGCTAATGTTCACCAGTCTCTTATAAGTTCCTGGCTCAGCACTGATCCTGC
AAAAGACCGTATTGAAATCACAAGTTTGCTTCCCAATAAGACTTTGTCCGTGAACAGTTTGGATGTTTTAGGTCCTTGTC
TTGTTTGTGGAACTGATGCAGAAGCAATTTATGTTACTAGACAACTTTTTTCA

Alignment

ORF - retro_tsyr_267 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.74 %
• Parental protein coverage: 89.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLTLPPAVALGMEEIYAKFVSQKISKTRWRPVPSGSLQTAETFATGSWDNEENYVSLWSIGDFGNLDSDG
          .LTLPPAVALGMEEIYAKFVSQKISKTRWRPVPSGSLQTAETFATGSWDNEENYVSLWSIGDFGNLDSDG
Retrocopy VLTLPPAVALGMEEIYAKFVSQKISKTRWRPVPSGSLQTAETFATGSWDNEENYVSLWSIGDFGNLDSDG

Parental  GFEGDHQLLCDIRHHGDVMDLQFFDQERIVAASSTGSVTVFLHHPNNQTLSVNQQWTAAHYHTGPGSPSY
          GFEGDHQLLCDIRHHGDVMDLQFFDQERIVAASSTGSVTVFLHHPNNQTLSVNQQWTAAHYHTGPGSPSY
Retrocopy GFEGDHQLLCDIRHHGDVMDLQFFDQERIVAASSTGSVTVFLHHPNNQTLSVNQQWTAAHYHTGPGSPSY

Parental  SSAPCTGIVCSNPEIVTVGEDGRINFFRADHKEALRTIDNADSSTLHAVTFLRTPEILTVNSIGQLKIWD
          SSAPCTGIVCSNPEIVTVGEDGRINFFRADHKEALRTIDNADSSTLHAVTFLRTPEILTVNSIGQLKIWD
Retrocopy SSAPCTGIVCSNPEIVTVGEDGRINFFRADHKEALRTIDNADSSTLHAVTFLRTPEILTVNSIGQLKIWD

Parental  FRQQGNEPSQILSLTGDRVPLHCVDRHPNQQHVVATGGQDGMLSIWDVRQGTMPVSLLKAHEAEMWEVHF
          FRQQGNEPSQILSLTGDRVPLHCVDRHPNQQHVVATGGQDGMLSIWDVRQGTMPVSLLKAHEAEMWEVHF
Retrocopy FRQQGNEPSQILSLTGDRVPLHCVDRHPNQQHVVATGGQDGMLSIWDVRQGTMPVSLLKAHEAEMWEVHF

Parental  HPSNPDHLFTCSEDGSLWHWDASTDVPEKSSLFHQGGRTSTFLSHSISNQANVHQSLISSWLSTDPAKDR
          HPSNPDHLFTCSEDGSLWHWDASTDVPEKSSLFHQGGRTSTFLSHSISNQANVHQSLISSWLSTDPAKDR
Retrocopy HPSNPDHLFTCSEDGSLWHWDASTDVPEKSSLFHQGGRTSTFLSHSISNQANVHQSLISSWLSTDPAKDR

Parental  IEITSLLPNKTLSVNSLDVLGPCLVCGTDAEAIYVTRQLFS
          IEITSLLPNKTLSVNSLDVLGPCLVCGTDAEAIYVTRQLFS
Retrocopy IEITSLLPNKTLSVNSLDVLGPCLVCGTDAEAIYVTRQLFS

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_267 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009426	1 retrocopy	retro_chof_1765,
Cavia porcellus	ENSCPOG00000010815	1 retrocopy	retro_cpor_481,
Macaca mulatta	ENSMMUG00000009830	1 retrocopy	retro_mmul_1962,
Monodelphis domestica	ENSMODG00000016808	2 retrocopies	retro_mdom_199, retro_mdom_353,
Ictidomys tridecemlineatus	ENSSTOG00000013449	1 retrocopy	retro_itri_990,
Tarsius syrichta	ENSTSYG00000000944	1 retrocopy	retro_tsyr_267 ,