RetrogeneDB ID: retro_itri_1573

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393551.1:1918548..1919238(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF141
• Ensembl ID: ENSSTOG00000019740
• Aliases: None
• Description: ring finger protein 141 [Source:HGNC Symbol;Acc:21159]

Sequence

>retro_itri_1573
ATGGGACAGCAAATTTCGGATCAGACACAGTTGGTTATTAACAAGTTACTAGAAAAAGTAGCAAAACACGTCATATTGGT
TCGAGAAAGTAGCTCCTTAACTTATGAAGAATTTCTTGGGAGAGTAGCTGAACTAAATGATGTAACTGCTAAAGTGGCTT
CTGGCCAGGAAAAACATCTTCTCTTTGAGGTACAACCTGGGTCTGATTCTTCTGCCTTTTGGAAAGTGGTTGTACGCGTG
GTCTGTACCAAGATTAACAAAAGCACTGGCATTGTGGAAGCATCACGGATCATGAATTTATACCAGTTTATTCAGCTTTA
TAAGGACATCACAAGTCAAGCAGTAGGAGTGTTGGCTCAGAGCTCCACCTCTGAAGAAGCTGATGAGAACTCATCTTCTG
TAACATCATGTCAGGCTAGTCTTTGGATGGGAAGGGTGAAGCAGCTGACCGATGAGGAGGAGTGTTGTATCTGTATGTAT
GGGCTGGCTGACCTCATCCTGCCTTGTGCTCACAGCTTTTGTCAGAAGTGTATTGATAAATGGAGTGATTGACACAGGAA
TTGCCCTATTTGTCGCCTGCAGATGACTGGAGCAAACGAATCTTGGGTGGTGTCAGATGGACCTACTGAAGATGATATGG
CTAACTGTATTCTTAACATGGCTGATGAAGCAGGCCAGCCCCTTAGGCCA

Alignment

ORF - retro_itri_1573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGQQISDQTQLVINKLPEKVAKHVILVRESSSLTYEEFLGRVAELNDVTAKVASGQEKHLLFEVQPGSDS
          MGQQISDQTQLVINKL.EKVAKHVILVRESSSLTYEEFLGRVAELNDVTAKVASGQEKHLLFEVQPGSDS
Retrocopy MGQQISDQTQLVINKLLEKVAKHVILVRESSSLTYEEFLGRVAELNDVTAKVASGQEKHLLFEVQPGSDS

Parental  SAFWKVVVRVVCTKINKSTGIVEASRIMNLYQFIQLYKDITSQAAGVLAQSSTSEEADENPSSVTSCQAS
          SAFWKVVVRVVCTKINKSTGIVEASRIMNLYQFIQLYKDITSQA.GVLAQSSTSEEADEN.SSVTSCQAS
Retrocopy SAFWKVVVRVVCTKINKSTGIVEASRIMNLYQFIQLYKDITSQAVGVLAQSSTSEEADENSSSVTSCQAS

Parental  LWMGRVKQLTDEEECCICMDGRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESWVVSDAPTE
          LWMGRVKQLTDEEECCICM.G.ADLILPCAHSFCQKCIDKWSD.HRNCPICRLQMTGANESWVVSD.PTE
Retrocopy LWMGRVKQLTDEEECCICMYGLADLILPCAHSFCQKCIDKWSD*HRNCPICRLQMTGANESWVVSDGPTE

Parental  DDMANYILNMADEAGQPLRP
          DDMAN.ILNMADEAGQPLRP
Retrocopy DDMANCILNMADEAGQPLRP

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_1573 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1573 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011014	1 retrocopy	retro_cjac_3999,
Cavia porcellus	ENSCPOG00000007808	2 retrocopies	retro_cpor_175, retro_cpor_198,
Macropus eugenii	ENSMEUG00000014558	1 retrocopy	retro_meug_1251,
Mus musculus	ENSMUSG00000030788	1 retrocopy	retro_mmus_2996,
Oryctolagus cuniculus	ENSOCUG00000002807	1 retrocopy	retro_ocun_1507,
Otolemur garnettii	ENSOGAG00000001765	1 retrocopy	retro_ogar_1262,
Sarcophilus harrisii	ENSSHAG00000002101	2 retrocopies	retro_shar_148, retro_shar_694,
Ictidomys tridecemlineatus	ENSSTOG00000019740	1 retrocopy	retro_itri_1573 ,