RetrogeneDB ID: retro_itri_1302

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393432.1:846046..846679(-)
• Located in intron of: ENSSTOG00000001441

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSSTOG00000012486
• Aliases: None
• Description: fibrillarin [Source:HGNC Symbol;Acc:3599]

Sequence

>retro_itri_1302
ACGCTCAACATGGTGCCCGGCTTCTCGGTGTACGGCGAGAAGCGCGTCACGGTGACCGAGAACGGCGTGAAGCAGGAGTA
CCGCACGTGGAACCCCTTCCGCTCCAAGCTGGCCGCGGCCATCCTGGGCGGGGTCGACCAGATCCACATCAAGCCCAAGT
CCAAGGTGCTGTACCTGGGCGCCGCCTCGGGGACCACCGTCTCCCACGTCTCCGACATCATCGGCCCCGACGGCCTGGTC
TACGCAGTCGAGTTCTCCCACCGCGCCGGCCGCGATCTGGTCAACGTGGCCAAGACGAGAACCAACATCATCCCGGTGCT
GGAGGACGCCCGGCACCCGCTCAAGTACCGCATGCTCATCGGCATGGTGGACGTGATCTTCGCAGACGTAGCCCAGCCAG
ACCAGTCGCGCATCGTGGCTCTGAACGCCCACACGTTCCTGCGCAACGGGGGCCACTTTCTCATTTCCATCAAAGCCAAC
TGCATAGACTCCACCGCGTCTGCAGAGGCTGTGTTTGCTTCTGAGGTGAGGAAGTTGCAGCAGGAGAACCTGAAGCCTCA
AGAGCAGCTGACCCTGGAGCCTTATGAGAGGGACCATGCTGTGGTCGTCGGGGTCTACCGGCCCCTTCCCAAG

Alignment

ORF - retro_itri_1302 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.73 %
• Parental protein coverage: 66.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHV
          T.N.VPG.SVYGEKRV...E...K.EYR.WNPFRSKLAAAILGGVDQIHIKP..KVLYLGAASGTTVSHV
Retrocopy TLNMVPGFSVYGEKRVTVTENGVKQEYRTWNPFRSKLAAAILGGVDQIHIKPKSKVLYLGAASGTTVSHV

Parental  SDIVGQDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVA
          SDI.G.DGLVYAVEFSHR.GRDL.N.AK.RTNIIPV.EDARHP.KYRMLI.MVDVIFADVAQPDQ.RIVA
Retrocopy SDIIGPDGLVYAVEFSHRAGRDLVNVAKTRTNIIPVLEDARHPLKYRMLIGMVDVIFADVAQPDQSRIVA

Parental  LNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPP
          LNAHTFLRNGGHF.ISIKANCIDSTASAEAVFASEV.K.QQEN.KPQEQLTLEPYERDHAVVVGVYRP.P
Retrocopy LNAHTFLRNGGHFLISIKANCIDSTASAEAVFASEVRKLQQENLKPQEQLTLEPYERDHAVVVGVYRPLP

Parental  K
          K
Retrocopy K

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_1302 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1302 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023221	1 retrocopy	retro_ecab_308,
Loxodonta africana	ENSLAFG00000000171	1 retrocopy	retro_lafr_23,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sorex araneus	ENSSARG00000008709	1 retrocopy	retro_sara_768,
Ictidomys tridecemlineatus	ENSSTOG00000012486	1 retrocopy	retro_itri_1302 ,
Tursiops truncatus	ENSTTRG00000003967	1 retrocopy	retro_ttru_30,