RetrogeneDB ID: retro_itri_822

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393328.1:9070134..9070554(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC34
• Ensembl ID: ENSSTOG00000023255
• Aliases: None
• Description: cell division cycle 34 [Source:HGNC Symbol;Acc:1734]

Sequence

>retro_itri_822
AAGGCACATATTAAATTTCCTATTGACTACCCATATTCACCACCTACCTTCAGATTCTTGACCAAAATGTGGCACCCCAA
CATTTATGAGAATGGAGATGTATGCCCTTGGATACTCCATCCTCCTGTAGATGACCCACAGAGTGGAGAACTGCCCTCTG
AAAGGCGGAATCCTACTCAGAATGTGAGGACTATTCTGTTAAGTGGAATCTCACTGCTTAGTGAGCCCAACACCTTCTCC
CCAGCCAATGTGGATGCTTCGGTTATGTTCAGGAAATGGAGGGACAGTAAAGGAAAAGACAAAGAATACGCTGAAATCAT
TAGGAAACAGGTTTCAGCCACTAAAGCCGAAGCAGAAAAGGATGGAGTGAAGGTCCCCACAACCCTGGCGGAATACTGCA
TCAAAACTAAAGTGCCTTCC

Alignment

ORF - retro_itri_822 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.86 %
• Parental protein coverage: 79.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QARLKFPIDYPYSPPAFRFLTKMWHPNIYETGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVI
          .A..KFPIDYPYSPP.FRFLTKMWHPNIYE.GDVC..ILHPPVDDPQSGELPSER.NPTQNVRTILLS.I
Retrocopy KAHIKFPIDYPYSPPTFRFLTKMWHPNIYENGDVCPWILHPPVDDPQSGELPSERRNPTQNVRTILLSGI

Parental  SLLNEPNTFSPANVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPA
          SLL.EPNTFSPANVDASVM.RKW..SKGKD.EY..IIRKQV..TK..AE.DGVKVPTTLAEYC.KTK.P.
Retrocopy SLLSEPNTFSPANVDASVMFRKWRDSKGKDKEYAEIIRKQVSATKAEAEKDGVKVPTTLAEYCIKTKVPS

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_822 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_822 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023874	1 retrocopy	retro_cpor_743,
Macropus eugenii	ENSMEUG00000000812	1 retrocopy	retro_meug_1683,
Mus musculus	ENSMUSG00000020307	1 retrocopy	retro_mmus_23,
Ochotona princeps	ENSOPRG00000001017	1 retrocopy	retro_opri_464,
Pan troglodytes	ENSPTRG00000010153	1 retrocopy	retro_ptro_52,
Rattus norvegicus	ENSRNOG00000008348	1 retrocopy	retro_rnor_1464,
Ictidomys tridecemlineatus	ENSSTOG00000007968	1 retrocopy	retro_itri_1338,
Ictidomys tridecemlineatus	ENSSTOG00000023255	1 retrocopy	retro_itri_822 ,
Tursiops truncatus	ENSTTRG00000000391	2 retrocopies	retro_ttru_1142, retro_ttru_98,