RetrogeneDB ID: retro_itri_900

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393340.1:933963..934187(-)
• Located in intron of: ENSSTOG00000001120

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V2
• Ensembl ID: ENSSTOG00000021769
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 variant 2 [Source:HGNC Symbol;Acc:12495]

Sequence

>retro_itri_900
TTAGAAGAGGATGAGCATGAAACACCTAAAAGGTGGACAGGCGTGATGACTGGGACACCAAGGACAGACTATGAAGACAA
AAGGTATAAGCTGTTAAAGCAGGATGTGAATACTGAGCACTCAGAGGCTCCTTCCTCAGATCTGTAATTTGGATTAATAA
ACCACTTAATAATTCCAGTGGGACAGTGGGTGCACGGAGTACCCCAGAGCTAGTAAAATGGCAG

Alignment

ORF - retro_itri_900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.28 %
• Parental protein coverage: 52.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LEDDEDMTLTRWTGMIIGPPRTNYENRIYSL-KVECGPKYPEAPPS-VRFVTKINMNGINNSSGMVDARS
          LE.DE..T..RWTG...G.PRT.YE...Y.L.K........EA.PS..R.V..IN....NNSSG.V.ARS
Retrocopy LEEDEHETPKRWTGVMTGTPRTDYEDKRYKLLKQDVNTEHSEA-PS<LRSVIWIN-KPLNNSSGTVGARS

Parental  IPVLAKWQ
          .P.L.KWQ
Retrocopy TPELVKWQ

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_900 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_900 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023218	1 retrocopy	retro_btau_902,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Pongo abelii	ENSPPYG00000018575	1 retrocopy	retro_pabe_2739,
Ictidomys tridecemlineatus	ENSSTOG00000014322	6 retrocopies	retro_itri_1001, retro_itri_1002, retro_itri_1134, retro_itri_1452, retro_itri_1600, retro_itri_992,
Ictidomys tridecemlineatus	ENSSTOG00000021769	2 retrocopies	retro_itri_568, retro_itri_900 ,