RetrogeneDB ID: retro_itri_467

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393293.1:6088373..6088604(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000010338
• Aliases: None
• Description: None

Sequence

>retro_itri_467
CTGCTCTAAGAACACCAGGCCTAGCAGAAGGGGCACAAGGAGCTGCAGAAGAAGATGAGGCGCGAGACTATCACTGCAGC
TACCTTCCTGGCAGAAGCTTTGGTGGATCACCTCATTGTGGGTGTTGCCCAGGCCTGCACGAACCAGAGAAAGCTGGACC
ATGAGTCCCTTCAAGTCCAGGCTGCCAAATCTGCCAAGTAGACAGGCCAGTGGATCAAGATGGAGGAGAAC

Alignment

ORF - retro_itri_467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.42 %
• Parental protein coverage: 63.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLKEHQAKQNERKELQEKRRREAITAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQFAKQT
          LL.EHQA.Q...KELQ.K.RRE.ITAAT.L.EALVDHL.VGVAQA..NQRKLDHE...LQVQAA..AK.T
Retrocopy LL*EHQA*QKGHKELQKKMRRETITAATFLAEALVDHLIVGVAQACTNQRKLDHE--SLQVQAAKSAK*T

Parental  GQWIGMVEN
          GQWI.M.EN
Retrocopy GQWIKMEEN

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_467 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_467 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011918	1 retrocopy	retro_btau_878,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148,
Cavia porcellus	ENSCPOG00000001818	2 retrocopies	retro_cpor_1260, retro_cpor_846,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Oryctolagus cuniculus	ENSOCUG00000010114	1 retrocopy	retro_ocun_1023,
Sus scrofa	ENSSSCG00000000359	1 retrocopy	retro_sscr_850,
Ictidomys tridecemlineatus	ENSSTOG00000010338	1 retrocopy	retro_itri_467 ,