RetrogeneDB ID: retro_itri_1198

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393398.1:3685311..3685577(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022476
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK2AP1
• Ensembl ID: ENSSTOG00000016464
• Aliases: None
• Description: cyclin-dependent kinase 2 associated protein 1 [Source:HGNC Symbol;Acc:14002]

Sequence

>retro_itri_1198
GGAAGTGTCCACTCACCTTCCACCAGCATGGCAGCAGCCTCCCAGTACCGCCAGCTGCTGAGTGACTATGGGCCACCATC
GCTGGGCTACACCCAGGGAACGGGAATAGCCAGGTGCCCCAGAGCAAGTATGCGGAACTGCTGGCCATCATGGAAGAGCT
GGGGAAGGAGATAAGACCTGCCTATGCAGGGAGCAAGAGCGCCATGGAGAGACTAAAACGCATCATTCACACACGAGGAC
TGGTTCTGGAGTGCTTGGCTGAAACG

Alignment

ORF - retro_itri_1198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 89.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSVHSPSTSMAASSQYRQLLSDYGPPSLGYTQGT-GNSQVPQSKYAELLAIIEELGKEIRPTYAGSKSAM
          GSVHSPSTSMAA.SQYRQLLSDYGPPSLGYTQGT.GNSQVPQSKYAELLAI.EELGKEIRP.YAGSKSAM
Retrocopy GSVHSPSTSMAAASQYRQLLSDYGPPSLGYTQGT<GNSQVPQSKYAELLAIMEELGKEIRPAYAGSKSAM

Parental  ERLKRGIIHARGLVRECLAET
          ERLKR.IIH.RGLV.ECLAET
Retrocopy ERLKR-IIHTRGLVLECLAET

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_1198 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1198 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015147	1 retrocopy	retro_amel_19,
Choloepus hoffmanni	ENSCHOG00000010939	1 retrocopy	retro_chof_56,
Gorilla gorilla	ENSGGOG00000009567	1 retrocopy	retro_ggor_1968,
Macropus eugenii	ENSMEUG00000009438	12 retrocopies	retro_meug_1101, retro_meug_1112, retro_meug_1218, retro_meug_1366, retro_meug_1509, retro_meug_1565, retro_meug_2116, retro_meug_377, retro_meug_404, retro_meug_669, retro_meug_836, retro_meug_868,
Monodelphis domestica	ENSMODG00000012451	2 retrocopies	retro_mdom_1845, retro_mdom_611,
Mus musculus	ENSMUSG00000029394	1 retrocopy	retro_mmus_125,
Rattus norvegicus	ENSRNOG00000001070	3 retrocopies	retro_rnor_1717, retro_rnor_1718, retro_rnor_1753,
Sarcophilus harrisii	ENSSHAG00000015009	1 retrocopy	retro_shar_366,
Ictidomys tridecemlineatus	ENSSTOG00000016464	1 retrocopy	retro_itri_1198 ,