RetrogeneDB ID: retro_tbel_2595

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_113666:8181..8825(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX7
• Ensembl ID: ENSTBEG00000000168
• Aliases: None
• Description: sorting nexin 7 [Source:HGNC Symbol;Acc:14971]

Sequence

>retro_tbel_2595
CCATTGTCAGAAACATTTGGAGTGAAAGGAATGGTGGAACGCTTTAATAATGACTTCATTGAGACATGCAGAAAAGCATT
ACACAAATTTTAGAACTGAATTGCTAATCATCTGACTTTAACATTTAATGAAGACTTCAAAGCTGTTCTCACAGCACAAG
CTTGGGAACTCTCTTTGCACCAGAAGCAAAGGCCTGGTTTGCTAAGCAGGATGTGGCCAACAGTCAGAGCTGTTGCCTCA
ATGAGAGGAATCGAAAACCCCCAGAGGAGTTCATGGAAATGAATAACTTTATTGAAATATTTAGCCAGAAAACAAATGTG
ATAGCTAAAATATCTCAGAGAATTTACAAGGAAGAAAGAGAATATTTTGATTAAATAAAAAAATATGGCCAAATTCATAT
TTTATGGTTAGCATCAGAAAAGGGTCTGGTTGATACTCTAAAAGGTATTGACAACTACATCAACAGATGCTGCAAGGACA
CTGAAAAAATGTGTGGGCTCTCAGAGGCACAGCTTCTTGTTGTACATGAGGATATACTTTACAGTGAAATGTTCATGGCT
GCTATGAAAAGGCCAGACCAGATTCAAGCTGCACTGGATTCCAAAGTTGAAGCTTTGACCTATTAAACAGCAGATACTGA
TCTG

Alignment

ORF - retro_tbel_2595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.23 %
• Parental protein coverage: 56.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PLPEKFIVKGMVERFNDDFIETRRKALQKFLNRIADHPTLTFNEDFKVFLTAQAWELSSHKKQGPGFLSR
          PL.E.F.VKGMVERFN.DFIET.RKAL.KF.N.IA.H.TLTFNEDFK..LTAQAWELS.H.KQ.PG.LSR
Retrocopy PLSETFGVKGMVERFNNDFIETCRKALHKF*N*IANHLTLTFNEDFKAVLTAQAWELSLHQKQRPGLLSR

Parental  MGQTVRAVASSVRGVKNR-PEEFMEMNHFIEIFSQKINLIDKISQRIYKEEREYFDEMKEYGPVHILWSA
          M..TVRAVAS..RG..N..PEEFMEMN.FIEIFSQK.N.I.KISQRIYKEEREYFD..K.YG..HILW.A
Retrocopy MWPTVRAVAS-MRGIENP<PEEFMEMNNFIEIFSQKTNVIAKISQRIYKEEREYFD*IKKYGQIHILWLA

Parental  SEEDLVDILKGIANCIDRCCKATEKRMFGLSEVLLPVVHEYVLYSEMLMAVMKRRDQIQAELDSKVEALT
          SE..LVD.LKGI.N.I.RCCK.TEK.M.GLSE..L.VVHE..LYSEM.MA.MKR.DQIQA.LDSKVEALT
Retrocopy SEKGLVDTLKGIDNYINRCCKDTEK-MCGLSEAQLLVVHEDILYSEMFMAAMKRPDQIQAALDSKVEALT

Parental  YKKADTDL
          Y..ADTDL
Retrocopy Y*TADTDL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_2595 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2595 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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
Bos taurus	ENSBTAG00000031461	1 retrocopy	retro_btau_453,
Choloepus hoffmanni	ENSCHOG00000008131	2 retrocopies	retro_chof_1097, retro_chof_1388,
Gorilla gorilla	ENSGGOG00000023577	1 retrocopy	retro_ggor_744,
Macropus eugenii	ENSMEUG00000011320	1 retrocopy	retro_meug_1016,
Sarcophilus harrisii	ENSSHAG00000002487	1 retrocopy	retro_shar_420,
Tupaia belangeri	ENSTBEG00000000168	1 retrocopy	retro_tbel_2595 ,