RetrogeneDB ID: retro_itri_239

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:10990222..10990598(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLNS1A
• Ensembl ID: ENSSTOG00000027980
• Aliases: None
• Description: chloride channel, nucleotide-sensitive, 1A [Source:HGNC Symbol;Acc:2080]

Sequence

>retro_itri_239
AAGAGCCTCAGTATCAGCACCTTTTACATTGCTGAGAGCCGCCTGTCTTGGTTAGGTGGTTCTGGATTAGGATTCTCACT
GGAATATTCCATTAGTTTACAAGCACTATCCTGAGAACTAATTGCCTATTCTCAAGAGCATTTGTATGTTGTGGTGAATA
ACAAATTTGGAGAAGAATCAAAAGAATCTTTCTCTGATGAAGAGAAGGAAGACCGCAATGATGTCAAACCTATTACATGA
TTTTAGGTTTGTGCCGAGTGATAAACCAGCATTGGAGGCAATATTCACTGCAATGTGTGAATGCCAGTCTTTGCATCCAG
ATCTAGATCCTGAAGATGAAGACTCAGATGAATTATATGATGGAGAAGAACAGGAA

Alignment

ORF - retro_itri_239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.66 %
• Parental protein coverage: 52.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGLGIGTLYIAESRLSWLDGSGLGFSLEYPTISLHAVSRDLNAYPREHLYVMVNAKFGEESKESLADEEE
          K.L.I.T.YIAESRLSWL.GSGLGFSLEY..ISL.A.S..L.AY..EHLYV.VN.KFGEESKES..DEE.
Retrocopy KSLSISTFYIAESRLSWLGGSGLGFSLEY-SISLQALS*ELIAYSQEHLYVVVNNKFGEESKESFSDEEK

Parental  EDSDDDVEPIT-EFRFVPSDKSALEVMFTAMCECQALHP--DPEDEDSDD-YDGEEYD
          ED...DV.PIT..FRFVPSDK.ALE..FTAMCECQ.LHP..DPEDEDSD..YDGEE..
Retrocopy EDR-NDVKPIT>DFRFVPSDKPALEAIFTAMCECQSLHPDLDPEDEDSDELYDGEEQE

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_239 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_239 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 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019930	1 retrocopy	retro_btau_376,
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Homo sapiens	ENSG00000074201	2 retrocopies	retro_hsap_3010, retro_hsap_3595,
Gorilla gorilla	ENSGGOG00000003091	1 retrocopy	retro_ggor_2084,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Mus musculus	ENSMUSG00000025439	1 retrocopy	retro_mmus_1984,
Nomascus leucogenys	ENSNLEG00000016699	2 retrocopies	retro_nleu_300, retro_nleu_756,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Pongo abelii	ENSPPYG00000003712	1 retrocopy	retro_pabe_2494,
Sorex araneus	ENSSARG00000009460	2 retrocopies	retro_sara_247, retro_sara_682,
Ictidomys tridecemlineatus	ENSSTOG00000027980	3 retrocopies	retro_itri_239 , retro_itri_319, retro_itri_490,