RetrogeneDB ID: retro_itri_749

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393317.1:9991512..9991808(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021649
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBP1
• Ensembl ID: ENSSTOG00000005673
• Aliases: None
• Description: retinol binding protein 1, cellular [Source:HGNC Symbol;Acc:9919]

Sequence

>retro_itri_749
GTCACCTTCACTAGGTACTGGAAGCTGCTGGCCCATGGCATTCCAAGGAGTACTCATGCATACTTAATGTCAGTGTGGCC
TTGCATAAAACCAACCACTTGGCTGAAGCCAAAGAGATAGAGCAGGAGTGTGACCATGCAATCATCTGGACACTGAGCAC
TTTCAGGAAGTACATCATGGACTTCTGTGTTGAGAAGGAGTTTAAGGAGGACCCAATGGGCATAGATAACACAAGCATGA
CCACAGTGATCTGGAATGGGGACAAGCTCCAGTGTGGGTAGAAGAGCAAGAAGGAG

Alignment

ORF - retro_itri_749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.84 %
• Parental protein coverage: 74.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDFNGYWKMLANE-NFEEYLRALDVNVALRKIANLLKPDKEIVQEGDHMIIRTLSTFRNYIMDFEVGKEF
          V.F..YWK.LA......EY...L.V.VAL.K..N.L...KEI.QE.DH.II.TLSTFR.YIMDF.V.KEF
Retrocopy VTFTRYWKLLAHG<HSKEYSCILNVSVALHK-TNHLAEAKEIEQECDHAIIWTLSTFRKYIMDFCVEKEF

Parental  EEDLTGIDDRKCMTTVNWDGDKLECVQKGEKE
          .ED..GID....MTTV.W.GDKL.C..K..KE
Retrocopy KEDPMGIDNTS-MTTVIWNGDKLQCG*KSKKE

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_749 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_749 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020028	1 retrocopy	retro_btau_1290,
Erinaceus europaeus	ENSEEUG00000005367	1 retrocopy	retro_eeur_42,
Macropus eugenii	ENSMEUG00000003195	2 retrocopies	retro_meug_1379, retro_meug_511,
Ictidomys tridecemlineatus	ENSSTOG00000003842	3 retrocopies	retro_itri_1544, retro_itri_640, retro_itri_641,
Ictidomys tridecemlineatus	ENSSTOG00000005673	1 retrocopy	retro_itri_749 ,
Ictidomys tridecemlineatus	ENSSTOG00000007877	3 retrocopies	retro_itri_1305, retro_itri_389, retro_itri_72,