RetrogeneDB ID: retro_itri_1747

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393713.1:426716..427179(+)
• Located in intron of: ENSSTOG00000006355

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF11
• Ensembl ID: ENSSTOG00000020072
• Aliases: None
• Description: ring finger protein 11 [Source:HGNC Symbol;Acc:10056]

Sequence

>retro_itri_1747
ATGGGGAACTGCCTCAAATCCCCCACCTCGGATGACATCTCCCTGCTTCACAAGTCTCAGTCCGACCGGGCTAGCTTTGG
CGAGGGGATGGAGCCAGATCAGGAGCCGCTGCCACCATATCAGGAACAAGTTCCAGTTCCAGTTTATCATCCAACACCTA
GCCAAACTCAGCTACCAACTCAGCTGACTGAAGAGGAACAAATTAGGATAGCTCAAAGAATAGGCCTTAATCAGCATCTG
CCTAAAGGAGTTTATGACCCTGGAAGAGATGGATCCGAAAAAAAAGATCCGGGAGTGTGTGATCTGTATGATGGACTTTG
TTTATGGGGACCCAATTCGATTTCTGCCGTGCATGCACATCTATCACCTGGACTGTATAGATGACTGGTTGATGAGACCC
TTCACATGCCCCTCCTGCATGGAGCCAGTTGATGTAGCACTGCTCTCATCCTATGAGACTAAT

Alignment

ORF - retro_itri_1747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.9 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGNCLKSPTSDDISLLHESQSDRASFGEGTEPDQEPPPPYQEQVPVPVYHPTPSQTRLATQLTEEEQIRI
          MGNCLKSPTSDDISLLH.SQSDRASFGEG.EPDQEP.PPYQEQVPVPVYHPTPSQT.L.TQLTEEEQIRI
Retrocopy MGNCLKSPTSDDISLLHKSQSDRASFGEGMEPDQEPLPPYQEQVPVPVYHPTPSQTQLPTQLTEEEQIRI

Parental  AQRIGLIQHLPKGVYDPGRDGS-EKKIRECVICMMDFVYGDPIRFLPCMHIYHLDCIDDWLMRSFTCPSC
          AQRIGL.QHLPKGVYDPGRDGS....IRECVICMMDFVYGDPIRFLPCMHIYHLDCIDDWLMR.FTCPSC
Retrocopy AQRIGLNQHLPKGVYDPGRDGS>XXXIRECVICMMDFVYGDPIRFLPCMHIYHLDCIDDWLMRPFTCPSC

Parental  MEPVDVALLSSYETN
          MEPVDVALLSSYETN
Retrocopy MEPVDVALLSSYETN

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_1747 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1747 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000006072	1 retrocopy	retro_etel_873,
Homo sapiens	ENSG00000123091	1 retrocopy	retro_hsap_3925,
Gorilla gorilla	ENSGGOG00000004919	1 retrocopy	retro_ggor_2641,
Myotis lucifugus	ENSMLUG00000004439	1 retrocopy	retro_mluc_145,
Otolemur garnettii	ENSOGAG00000011682	1 retrocopy	retro_ogar_2003,
Pongo abelii	ENSPPYG00000001361	1 retrocopy	retro_pabe_3241,
Pan troglodytes	ENSPTRG00000041089	1 retrocopy	retro_ptro_2669,
Ictidomys tridecemlineatus	ENSSTOG00000020072	4 retrocopies	retro_itri_1747 , retro_itri_1886, retro_itri_633, retro_itri_974,
Tursiops truncatus	ENSTTRG00000010211	1 retrocopy	retro_ttru_1644,