RetrogeneDB ID: retro_itri_856

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393333.1:4926341..4927059(-)
• Located in intron of: ENSSTOG00000004318

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNH
• Ensembl ID: ENSSTOG00000000659
• Aliases: None
• Description: cyclin H [Source:HGNC Symbol;Acc:1594]

Sequence

>retro_itri_856
ATATACCACAACAGCAGCCAAGAGAGACGTTGGACTTTTGCCACTGAGGAGCAGCTGGCCCATCTGCAGGCCAACACTGA
TCACAAATTCAAATGCAAAGTGGTGGCAAAGGGGAAGTTTTTCCAAATGATCCAGTCTTTCTTGAGCCTCATGAAGAAAG
GACACTCTGCAAATACTATGAAAAAGATTACTAGAATTCTGTTCAGTGTTTAAGCCAGCAATGCCATGGTCTGTTGTAGG
TACAGCTTGCATGTATTTCAAGCGTTCAAGTTTTATCAATAACTCTGTAATGGAATATCACCCATGAATAATATTGCTTA
CTTGTTCATTTTGGGCTTGTAAAGTAGATGAATTCAATGTGTCTAGTCCTCAGTTTGTTGGAAACCTTCTAGAGAATCCT
CTTGGACAGAAGAAGGCACTGGAACAGATTTTGGAATAGGAGCTACTCCTTATAAAACAGCTTAATTTTCATCTTATTGT
CCACAATCATTATAGACAGTTTGAGTGCTTCCTCACTGATATAAAGACCCACTATCCCATGTTGGAGAATCCAGAGATTT
TGAGGAAAACAGCTGATGACTCTCTTAATAAAATTGCACTGACTAATGCTTATCTTTTATACATACCTTCTCAAATTGCC
TTGACTGTCATATTATCTAGTGCTTCCACTAGATAATTGCTAAGGGATTGCTATGAAAAGGTATTTATCAGAGAGTCT

Alignment

ORF - retro_itri_856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.46 %
• Parental protein coverage: 74.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MYHNSSQKRHWTFASEEQLARLRADANRKFKCKVVANGK-VLPNDPVFLEPHEEMTLCKYYEK-RLLEFC
          .YHNSSQ.R.WTFA.EEQLA.L.A....KFKCKVVA.GK.V.PNDPVFLEPHEE.TLCKYYEK.RLLEFC
Retrocopy IYHNSSQERRWTFATEEQLAHLQANTDHKFKCKVVAKGK<VFPNDPVFLEPHEERTLCKYYEK<RLLEFC

Parental  SVFKPAMPRSVVGTACMYFKRF-YLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPVGQE
          SVFKPAMP.SVVGTACMYFKR....NNSVMEYHP.II.LTC.F.ACKVDEFNVSSPQFVGNL.E.P.GQ.
Retrocopy SVFKPAMPWSVVGTACMYFKRSSFINNSVMEYHP*IILLTCSFWACKVDEFNVSSPQFVGNLLENPLGQK

Parental  KALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDIKTRYPMLENPEILRKTADDFLNRIALTDAYLLY
          KALEQILE.ELLLI.QLNFHLIVHN.YR.FE.FL.DIKT.YPMLENPEILRKTADD.LN.IALT.AYLLY
Retrocopy KALEQILE*ELLLIKQLNFHLIVHNHYRQFECFLTDIKTHYPMLENPEILRKTADDSLNKIALTNAYLLY

Parental  TPSQIALTAILSSASRAGIAMESYLSESLMLREN
          .PSQIALT.ILSSAS........Y..E....RE.
Retrocopy IPSQIALTVILSSASTR*LLRDCY--EKVFIRES

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_856 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_856 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007765	1 retrocopy	retro_dnov_1618,
Homo sapiens	ENSG00000134480	1 retrocopy	retro_hsap_3128,
Gorilla gorilla	ENSGGOG00000005172	1 retrocopy	retro_ggor_2143,
Macaca mulatta	ENSMMUG00000003248	1 retrocopy	retro_mmul_1991,
Mus musculus	ENSMUSG00000021548	1 retrocopy	retro_mmus_2510,
Nomascus leucogenys	ENSNLEG00000013604	1 retrocopy	retro_nleu_2248,
Oryctolagus cuniculus	ENSOCUG00000004659	1 retrocopy	retro_ocun_588,
Pongo abelii	ENSPPYG00000015619	2 retrocopies	retro_pabe_2584, retro_pabe_2590,
Pan troglodytes	ENSPTRG00000017063	1 retrocopy	retro_ptro_2116,
Ictidomys tridecemlineatus	ENSSTOG00000000659	1 retrocopy	retro_itri_856 ,