RetrogeneDB ID: retro_itri_12

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393459.1:203879..204623(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000003377
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM133B
• Ensembl ID: ENSSTOG00000028195
• Aliases: None
• Description: family with sequence similarity 133, member B [Source:HGNC Symbol;Acc:28629]

Sequence

>retro_itri_12
ATGGGAAAGCGGGATAACCGGGTGGCCTACATGAATCCTATAGCAATGGCCAGATGGAGGGGCCCAACTCAATCTGCAGG
CCCAACAATACAAGATTATCTGAATCGACCAAGGCCCACCTGGGAAGAAGTGAAGAAACAATTAGAAAACAAAAAGAAAG
GCTCCAAGGCCTTAGCTGAATTTGAAGAAAAAATGAATGAAAGTTGGAAGAAAGAGCTTGAAAAAAGCAGAGAGAAATTA
TTAAGTGGAAGTGAGAGTTCAACCAAAAAGAGAGAAAAAAAGAAAAAGAAAAAGAAGAAATCTTGTCAGTTGTCATCATC
TTCATCAAGTGCTGATTCTTCAAGCAGTTCTTCAGATTCAGAAAATGAAGAAAAGAAGCCAGGAAAAAAGAGAAAGAAAA
AGAAGAACCGCTCACACAAATCATCAGAATGCTCAACATCTGCACCAGAATCAGAGAGCAAGGAATCTGTAAAAAAGAAA
AAGAAGTCAAAGGTAGAAATAAGGAAAGAAAAGTGTATTAGAAGTCTCAGCAAAAAGAGAAAGAAAACTTATCCTGAGGA
TAAACCATCTTCATCTGAGTCTTCATCAGAATCAGATCATGAAGAGGAAGTACAAGCAAAAAAGAAGAGAAAGTGTGAAG
AGAAAGAAAAAGCAATAGAAAAAGTAAAGAAGAAAAAGAAACAACATAAGAAACATAGTAAAAAGAAAAAAAAGAAGTCT
GGTTCAAGTCACAAGTCAGGATAA

Alignment

ORF - retro_itri_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.63 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEKMNENWK
          MGKRDNRVAYMNPIAMAR.RGP.QS.GPTIQDYLNRPRPTWEEVK.QLE.KKKGSKALAEFEEKMNE.WK
Retrocopy MGKRDNRVAYMNPIAMARWRGPTQSAGPTIQDYLNRPRPTWEEVKKQLENKKKGSKALAEFEEKMNESWK

Parental  KELEKHREKLLSGNESSSKKRQRKKKEKKKSGRYSSSSSSSSDSSSSSSDSEDEDKKQTKRRKKKKNRSH
          KELEK.REKLLSG.ESS.KKR..KKK.KKKS....SSSSSS.DSSSSSSDSE.E.KK..K.RKKKKNRSH
Retrocopy KELEKSREKLLSGSESSTKKREKKKKKKKKSCQL-SSSSSSADSSSSSSDSENEEKKPGKKRKKKKNRSH

Parental  KSSESSTSETESDSKDSLKKKKKSKDATEKEKDIKGFSKKRKMN-PEDKPLSSESLSESDYIEEVRAKKK
          KSSE.STS..ES.SK.S.KKKKKSK....KEK.I...SKKRK...PEDKP.SSES.SESD..EEV.AKKK
Retrocopy KSSECSTSAPESESKESVKKKKKSKVEIRKEKCIRSLSKKRKKTYPEDKPSSSESSSESDHEEEVQAKKK

Parental  KSSEERDKA
          ...EE..KA
Retrocopy RKCEEKEKA

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_12 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_12 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 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12 ,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,