RetrogeneDB ID: retro_itri_1724

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393674.1:512044..512324(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG5
• Ensembl ID: ENSSTOG00000016507
• Aliases: None
• Description: autophagy related 5 [Source:HGNC Symbol;Acc:589]

Sequence

>retro_itri_1724
GAGTATCCTGCAGAAGAAAATGGATTTCATTATATCCCTTTTAGACTATATCAGACAACAACTGAACACCATTTCATTCA
GAAACTGTTTTGTGGGTGGCTGCAGATGGACAGCTATATACACTGGGCAATCTCCTCAAAGAAGTTTGTCCCTCTGTAAT
TACTCCTGAAGGTGGAGAAAGAAGGAATCAAGTGACAATTCATGGAATTGAGCCAATGTTGGAAACACCTCTGCAGCAGC
TAAGTGAAATCTGAGCTATCCGGATAATTCTCTTAGCATC

Alignment

ORF - retro_itri_1724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.21 %
• Parental protein coverage: 91.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EYPAEENGFRYIPFRIYQTTTERPFIQKLFRP-VAADGQPHTLGDLLKEVCPSAIAPEDGERRNQVMIHG
          EYPAEENGF.YIPFR.YQTTTE..FIQKLF...VAADGQ..TLG.LLKEVCPS.I.PE.GERRNQV.IHG
Retrocopy EYPAEENGFHYIPFRLYQTTTEHHFIQKLFCG<VAADGQLYTLGNLLKEVCPSVITPEGGERRNQVTIHG

Parental  IEPMLETPLQWLSE-HLSYPDNFLHI
          IEPMLETPLQ.LSE..LSYPDN.L.I
Retrocopy IEPMLETPLQQLSE<NLSYPDNSLSI

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_1724 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1724 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006399	1 retrocopy	retro_chof_1928,
Dasypus novemcinctus	ENSDNOG00000013004	2 retrocopies	retro_dnov_1805, retro_dnov_950,
Myotis lucifugus	ENSMLUG00000014090	1 retrocopy	retro_mluc_872,
Ictidomys tridecemlineatus	ENSSTOG00000016507	1 retrocopy	retro_itri_1724 ,