RetrogeneDB ID: retro_itri_906

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393341.1:7417981..7418686(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK5
• Ensembl ID: ENSSTOG00000016068
• Aliases: None
• Description: cyclin-dependent kinase 5 [Source:HGNC Symbol;Acc:1774]

Sequence

>retro_itri_906
CTGAAGCACAAGAACATCATCAGGCTTCATGATGCTCTGCATAGTGACAAGGAGCTGACTTTGGTTTTTGAGTTCTGTGA
TCAGGACCTGAAGAAGTATTTTGACAACTGCAATGGTGACCTCGATCCTGAGATTGTGAAGTCATTCCTTTTCCAGCTGC
TGATAGGCCTGGGATTCTGTCATAGCCGCAACGTGTTTCACAGGGTCCTGAAGCCCCAGAACCTCCTCATAAACAGAAAT
GGGGAGCTGAAGTTGGCTGATTTTGGTTTGGCTCAAGCCTTTAGGATCCCAGTCCGCTGTTACTCTGCTGAGGTGGTGAC
ATTGTGGTACCGTCCACCGGATGACCTCTTTGGGGCCAAACTGTACTTCACATCCATCGACATGTGGTCAGCTGGCTGCA
TCTTTGCCGAGCTGGCCAATGCTGGGCAACCTTTTTTCCTTGGCAACGATGTAGATGACCAGCTGAAGAGGATCTTCCAG
CTGCTGGGGACACCATCTGAGGAGCACTGGCCCGCCATGACTAAGCTGCCAGACTACAAGCCCTACCCAATGTACCCCGC
CACAACATCCCTGGTGAATGCCGTGCCCAAGCTCAATGCCACAGGGAGGGGCCTGTTGCAGAATCTCCTGAAGTGTAACC
CTGTCCAGCATGTCTCAGCGGAGGAGGCCCTGCAATACCCCTAATTCTCTGACTTCTGTCCCCCC

Alignment

ORF - retro_itri_906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.64 %
• Parental protein coverage: 80.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKHKNIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDL
          LKHKNI.RLHD.LHSDK.LTLVFEFCDQDLKKYFD.CNGDLDPEIVKSFLFQLL.GLGFCHSRNV.HR.L
Retrocopy LKHKNIIRLHDALHSDKELTLVFEFCDQDLKKYFDNCNGDLDPEIVKSFLFQLLIGLGFCHSRNVFHRVL

Parental  KPQNLLINRNGELKLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELAN
          KPQNLLINRNGELKLADFGLA.AF.IPVRCYSAEVVTLWYRPPD.LFGAKLY.TSIDMWSAGCIFAELAN
Retrocopy KPQNLLINRNGELKLADFGLAQAFRIPVRCYSAEVVTLWYRPPDDLFGAKLYFTSIDMWSAGCIFAELAN

Parental  AGRPLFPGNDVDDQLKRIFRLLGTPTEEQWPAMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLL
          AG.P.F.GNDVDDQLKRIF.LLGTP.EE.WPAMTKLPDYKPYPMYPATTSLVN.VPKLNATGR.LLQNLL
Retrocopy AGQPFFLGNDVDDQLKRIFQLLGTPSEEHWPAMTKLPDYKPYPMYPATTSLVNAVPKLNATGRGLLQNLL

Parental  KCNPVQRVSAEEALQHPYFSDFCPP
          KCNPVQ.VSAEEALQ.P.FSDFCPP
Retrocopy KCNPVQHVSAEEALQYP*FSDFCPP

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_906 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_906 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020258	1 retrocopy	retro_cjac_1522,
Homo sapiens	ENSG00000164885	1 retrocopy	retro_hsap_4002,
Gorilla gorilla	ENSGGOG00000016879	1 retrocopy	retro_ggor_2686,
Nomascus leucogenys	ENSNLEG00000004100	1 retrocopy	retro_nleu_549,
Pongo abelii	ENSPPYG00000018183	1 retrocopy	retro_pabe_3290,
Pan troglodytes	ENSPTRG00000019872	1 retrocopy	retro_ptro_2717,
Ictidomys tridecemlineatus	ENSSTOG00000016068	1 retrocopy	retro_itri_906 ,