RetrogeneDB ID: retro_tbel_2431

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_110613:222779..223331(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNPDA1
• Ensembl ID: ENSTBEG00000003330
• Aliases: None
• Description: glucosamine-6-phosphate deaminase 1 [Source:HGNC Symbol;Acc:4417]

Sequence

>retro_tbel_2431
AGCACCCTACTTTACTGCTATAGGAAGCTGATTGAATTCTGTAAGGAATTCCTGTCTTTTAAACATGGGAAGACCTTCAG
CATGGATGAGTATGTGGGTCTTCCTCTGAACCACTGGAGAATTACCACTCCTTCACAGGGAACACCTTCAAACACACTGA
CATCCAACTAGAAAATACCCACACGCTGGATGGTAAGGCAGCCAACCTACAGGCTGAATGTGATGCCTTTAAAGAGCAGA
TCAAGGATGCAGGTAGGATCGAGCTATTTGTTGGAGGCATTGGCCCCAATGGATCCATTGCCTTCAATGAGCCGGGCTCT
AGTCTGGTGTCCAGACTGGAGTGAAGAAGCAGGCCATCTACACCATGCTGGCTGATGTTAAGCTCTTTAGTGGAGATTTT
ATATAGGAGCCCACTCTGATCCTGACAGTGGGCATGGGCACTGTCATGGATGCTAGAGAGGTGATGATCCTCAATATAGG
CACTCACAAGGTATTGCTCTATAAAGGGTCATGGAAGAGGAAGTGAGTCATATGTGGACCGTGTCTGCCTTC

Alignment

ORF - retro_tbel_2431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.84 %
• Parental protein coverage: 87.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  STPLGCYKKLIEYYKNGDLSFKYVKTFNMDEYVGLPRDH-PESYHSFMWNNFFKHIDIDPENTHILDGNA
          ST.L.CY.KLIE..K...LSFK..KTF.MDEYVGLP..H..E.YHSF..N.F.KH.DI..ENTH.LDG.A
Retrocopy STLLYCYRKLIEFCKEF-LSFKHGKTFSMDEYVGLPLNH<LENYHSFTGNTF-KHTDIQLENTHTLDGKA

Parental  ADLQAECDAFEEKIKAAGGIELFVGGIGPDGHIAFNEPGSSLVSR-TRVKTLAMDTILANARFFDGDLAK
          A.LQAECDAF.E.IK.AG.IELFVGGIGP.G.IAFNEPGSSLVSR.T.VK..A..T.LA....F.GD...
Retrocopy ANLQAECDAFKEQIKDAGRIELFVGGIGPNGSIAFNEPGSSLVSR<TGVKKQAIYTMLADVKLFSGDFI*

Parental  VPTMALTVGVGTVMDAREVMILITGAHK-AFALYKAIEEGVNHMWTVSAF
          .PT..LTVG.GTVMDAREVMIL..G.HK...AL....EE.V.HMWTVSAF
Retrocopy EPTLILTVGMGTVMDAREVMILNIGTHK<GIAL*RVMEEEVSHMWTVSAF

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_2431 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2431 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007865	1 retrocopy	retro_btau_535,
Choloepus hoffmanni	ENSCHOG00000009884	2 retrocopies	retro_chof_2278, retro_chof_42,
Dasypus novemcinctus	ENSDNOG00000007804	3 retrocopies	retro_dnov_1363, retro_dnov_1608, retro_dnov_508,
Macropus eugenii	ENSMEUG00000015442	1 retrocopy	retro_meug_655,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337,
Mus musculus	ENSMUSG00000052102	1 retrocopy	retro_mmus_2711,
Oryctolagus cuniculus	ENSOCUG00000016963	1 retrocopy	retro_ocun_1266,
Otolemur garnettii	ENSOGAG00000007303	3 retrocopies	retro_ogar_2251, retro_ogar_2506, retro_ogar_446,
Ictidomys tridecemlineatus	ENSSTOG00000016508	1 retrocopy	retro_itri_1135,
Tupaia belangeri	ENSTBEG00000003330	2 retrocopies	retro_tbel_2431 , retro_tbel_59,