RetrogeneDB ID: retro_itri_1135

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393383.1:5197886..5198508(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000013201
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GNPDA1
• Ensembl ID: ENSSTOG00000016508
• Aliases: None
• Description: glucosamine-6-phosphate deaminase 1 [Source:HGNC Symbol;Acc:4417]

Sequence

>retro_itri_1135
CAGAGTTACCACTCTTTTATGTGGAACAACTTCTTCAAGCACATTGATATCCATCCAGAGAATACCCCACATTCTGCATG
GGAATTCAGCTGACCTGCAGGCTGAGTGTGATGCCTTTGAGCAGAAGATCAAGGATGCAGGTGGGATTGAGCTGTTTGCT
GGAGGCATTGGCCCTGATGGACATATTGCCTTCAATGAGCCAGGTTCCAGCCTGGTGTCCAGGATTTGTGTGAAGACAGT
ATCCATGGACACCATGCTGGCCAATGCTAGGTTCTTTGATGGTGATCTTGCCAAGGTGCCCACCATGGCCCTGACAGTGG
GTGTGGGCACTGTCATGGATGCTAGAGAGGTGATGATCCTCATCACAGGCGCTCACAAAACTTTTGCTTCGAACAAGGCC
ATCGAGGAAGGGGTGAAACGTATGTGGACCGTGTCTGCCTTCCAGCAGCATCCCTGCACCGTGTTTGTGTGTGATGAAGA
TGCCACCTTGGAGCCGAAAGTGAAGATTGTCAAGTATTTCAAAGGTTTAATGCTTGTTCATAACAAGTTGGTGGACCCCC
TGTACAGTATCAAAGAGAAAGAAATTGAGAAAAACCAGTCTTCTAAGAAACCATGCAGTGAT

Alignment

ORF - retro_itri_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.38 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESYHSFMWNNFFKHIDIHPENT-HILDGNAADLQAECDAFEQKIKAAGGIELFVGGIGPDGHIAFNEPGS
          .SYHSFMWNNFFKHIDIHPENT.HIL.GN.ADLQAECDAFEQKIK.AGGIELF.GGIGPDGHIAFNEPGS
Retrocopy QSYHSFMWNNFFKHIDIHPENT>HILHGNSADLQAECDAFEQKIKDAGGIELFAGGIGPDGHIAFNEPGS

Parental  SLVSRTRVKTLAMDTILANARFFDGDLAKVPTMALTVGVGTVMDAREVMILITGAHKAFALYKAIEEGVN
          SLVSR..VKT..MDT.LANARFFDGDLAKVPTMALTVGVGTVMDAREVMILITGAHK.FA..KAIEEGV.
Retrocopy SLVSRICVKTVSMDTMLANARFFDGDLAKVPTMALTVGVGTVMDAREVMILITGAHKTFASNKAIEEGVK

Parental  HMWTVSAFQQHPCTVFVCDEDATLELKVKTVKYFKGLMLVHNKLVDPLYSIKEKEIEKSQSSKKPYSD
          .MWTVSAFQQHPCTVFVCDEDATLE.KVK.VKYFKGLMLVHNKLVDPLYSIKEKEIEK.QSSKKP.SD
Retrocopy RMWTVSAFQQHPCTVFVCDEDATLEPKVKIVKYFKGLMLVHNKLVDPLYSIKEKEIEKNQSSKKPCSD

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1135 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1135 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 9 parental genes, and 15 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,
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,