RetrogeneDB ID: retro_itri_1186

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393395.1:3404971..3405428(-)
• Located in intron of: ENSSTOG00000005162

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPHOSPH6
• Ensembl ID: ENSSTOG00000019608
• Aliases: None
• Description: M-phase phosphoprotein 6 [Source:HGNC Symbol;Acc:7214]

Sequence

>retro_itri_1186
ACCAAGTTGTCCAAGAACCTGCTGTGCATGAAGTTCATGCAAAGGGGACTGGAACCAAGAAACAACTAGAAGAAGAAGAA
AAGAAAATCATCAGTGAAGAGCACTGGTACTTGGATTTGCCAAAGCTCAAAGAGAAAGAGAATGTCATAATAGAGGAGCA
GAGCTTCTTGTTATGTGAAGATCTTATGTATGGAAGAATGTAATTCAGAGGATTTAATCCTGAAGTTGAGAAATTGATGC
TTCAGATGAATGCTAAGAACAAAGCAGAAGATGAAGATGAAGATGAAATAGTAGAGATTGATGTGTCAGATGAGGAAATG
GCTAGAAGATATGAGACCTTGGTGGGGACAATTGGAAAAAAATTTGCCAAGAAAAGAGACCGTGCCAATTATGAAGAAGA
TGAAATGGAGACATACAACCAGTTAAAGCAAAGAAGATGTTCTTAAAGCCCCACAAT

Alignment

ORF - retro_itri_1186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 96.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TKLSKNLLRMKFMQRGLD-SETKKQLEEEEKKIISEEHWYLDLPELKEKESVIIEEQSFLLCEDLLYGRM
          TKLSKNLL.MKFMQRGL.........EE....IISEEHWYLDLP.LKEKE.VIIEEQSFLLCEDL.YGRM
Retrocopy TKLSKNLLCMKFMQRGLE<TKKQLEEEEKK--IISEEHWYLDLPKLKEKENVIIEEQSFLLCEDLMYGRM

Parental  SFRGFNPEVEKLMLQMNAKNKAEDEDEDEIVELDVSDEEMARRYETLVGTIGKKFAKKRDRANYEEDE-N
          .FRGFNPEVEKLMLQMNAKNKA.......IVE.DVSDEEMARRYETLVGTIGKKFAKKRDRANYEEDE.N
Retrocopy *FRGFNPEVEKLMLQMNAKNKAXXXXXXXIVEIDVSDEEMARRYETLVGTIGKKFAKKRDRANYEEDE<N

Parental  GNIKPVKAKKMFLKPQD
          G.I.PVKAKKMFLKP..
Retrocopy GDIQPVKAKKMFLKPHN

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_1186 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1186 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009746	1 retrocopy	retro_btau_591,
Echinops telfairi	ENSETEG00000010276	6 retrocopies	retro_etel_1269, retro_etel_1300, retro_etel_1307, retro_etel_749, retro_etel_795, retro_etel_855,
Macropus eugenii	ENSMEUG00000000580	1 retrocopy	retro_meug_726,
Myotis lucifugus	ENSMLUG00000000268	1 retrocopy	retro_mluc_78,
Mus musculus	ENSMUSG00000031843	2 retrocopies	retro_mmus_1998, retro_mmus_3662,
Oryctolagus cuniculus	ENSOCUG00000024341	2 retrocopies	retro_ocun_1042, retro_ocun_749,
Rattus norvegicus	ENSRNOG00000050087	6 retrocopies	retro_rnor_1760, retro_rnor_2298, retro_rnor_2318, retro_rnor_2320, retro_rnor_2390, retro_rnor_2391,
Ictidomys tridecemlineatus	ENSSTOG00000019608	1 retrocopy	retro_itri_1186 ,
Tupaia belangeri	ENSTBEG00000013110	8 retrocopies	retro_tbel_1037, retro_tbel_1812, retro_tbel_3027, retro_tbel_32, retro_tbel_333, retro_tbel_4213, retro_tbel_4385, retro_tbel_4415,