RetrogeneDB ID: retro_tbel_2374

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109675:381..1350(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT7
• Ensembl ID: ENSTBEG00000012122
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) [Source:HGNC Symbol;Acc:4129]

Sequence

>retro_tbel_2374
GTCATGTCCTCCCATAATGAAGGATGGTCAACCCTCATGAGAACCGTCCCAGTGTATAAAAGGACTCCAAGGAATATTTA
GCAGAAATGTGTTAATTGATGATTTCAGCAATAAAGAACACTAAAAGAAAGACTGGATGAGTACATTAAAATGTGGAATG
GCCTAGTGAAAGTATTTCGAAATGAGAGAAGAGAAGGTTTAATTCAAGCACGAAGTATTGGTGCTCAGAAGGCTAAACTT
GGACAGGTGCTGATATACCTTGACGCCCACTGTGAGGTGGCAGTTAACTGGTACGCACCACTTGTAGCTCCCATATCTAA
GGACAGAACCATTTGCACTGTGCCGATTATAGATGTCATAAATGGCAACACATATGAAATTGTACCCCAAGGGGGTGGTG
ATGAAGATGGGTATGCCCGAGGAGCATGGGATTGGAGTATGCTCTGGAAACGGGTGCCTCTGACCTCTCGAGAGAAGAAA
CTGAGAAAGACAAAAACTGAACCGTATCGGTCCCCAGCCATGGCTGGTGGATTATTTGCCATTGAACGAGAATTCTTCTT
TGAGCTGGGTCTCTATGATCCAGGTCTGCAGATTTGGGGTGGCGAAAACTTTGAGATCTCATACAAGATATGGCAGTGTG
GTGGCAAATTACTGTTTGTCCCTTGTTCTCGTGTGGGACATATCTACCGTCTTGAGGGCTGGCAAGGAAACCCTCCACCT
GTGTATGTTGGGTCTTCTCCAACTCTAAAGAATTATATTAGAGTTGTAGAGGTTTGGTGGGATGAATATAAAGACTACTT
CTATGCTAGTCGTCCTGAATCAAAGGCGCTACCCTATGGAGATATATCTGAGCTGAAAAAATTTAGAGAAGATCACAACT
GCAAAAGTTTCAAGTGGTTTATGGAAGAAATAGCTTACGATATCACCTCACACTACCCTTTGCCACCCAGAAATATTGAC
TGGGGAGAA

Alignment

ORF - retro_tbel_2374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.65 %
• Parental protein coverage: 52.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VIVFHNEGWSTLMRTVHSVIKRTPR-KYLAEI-VLIDDFSNKEH-LKERLDEYIKMWNGLVKVFRNERRE
          V...HNEGWSTLMRTV..V.KRTPR..YLAE..VLIDDFSNKEH.LKERLDEYIKMWNGLVKVFRNERRE
Retrocopy VMSSHNEGWSTLMRTV-PVYKRTPR<EYLAEM<VLIDDFSNKEH<LKERLDEYIKMWNGLVKVFRNERRE

Parental  GLIQARSIGAQKAKLGQVLIYLDAHCEVAVNWYAPLVAPISKDRTICTVPIIDVINGNTYEIVPQGGGDE
          GLIQARSIGAQKAKLGQVLIYLDAHCEVAVNWYAPLVAPISKDRTICTVPIIDVINGNTYEIVPQGGGDE
Retrocopy GLIQARSIGAQKAKLGQVLIYLDAHCEVAVNWYAPLVAPISKDRTICTVPIIDVINGNTYEIVPQGGGDE

Parental  DGYARGAWDWSMLWKRVPLTSREKKLRKTKTEPYRSPAMAGGLFAIEREFFFELGLYDPGLQIWGGENFE
          DGYARGAWDWSMLWKRVPLTSREKKLRKTKTEPYRSPAMAGGLFAIEREFFFELGLYDPGLQIWGGENFE
Retrocopy DGYARGAWDWSMLWKRVPLTSREKKLRKTKTEPYRSPAMAGGLFAIEREFFFELGLYDPGLQIWGGENFE

Parental  ISYKIWQCGGKLLFVPCSRVGHIYRLEGWQGNPPPVYVGSSPTLKNYIRVVEVWWDEYKDYFYASRPESK
          ISYKIWQCGGKLLFVPCSRVGHIYRLEGWQGNPPPVYVGSSPTLKNYIRVVEVWWDEYKDYFYASRPESK
Retrocopy ISYKIWQCGGKLLFVPCSRVGHIYRLEGWQGNPPPVYVGSSPTLKNYIRVVEVWWDEYKDYFYASRPESK

Parental  ALPYGDISELKKFREDHNCKSFKWFMEEIAYDITSHYPLPPRNIDWGE
          ALPYGDISELKKFREDHNCKSFKWFMEEIAYDITSHYPLPPRNIDWGE
Retrocopy ALPYGDISELKKFREDHNCKSFKWFMEEIAYDITSHYPLPPRNIDWGE

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_2374 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2374 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007840	1 retrocopy	retro_cfam_220,
Monodelphis domestica	ENSMODG00000025055	1 retrocopy	retro_mdom_1409,
Tupaia belangeri	ENSTBEG00000000869	1 retrocopy	retro_tbel_1671,
Tupaia belangeri	ENSTBEG00000003627	1 retrocopy	retro_tbel_2065,
Tupaia belangeri	ENSTBEG00000012122	1 retrocopy	retro_tbel_2374 ,