RetrogeneDB ID: retro_itri_1316

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393439.1:3252834..3253286(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025303
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSSTOG00000002417
• Aliases: None
• Description: ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]

Sequence

>retro_itri_1316
TCTCTAGTGATTCCTGAAAAGTTCCAGCACATTTTGCGAGTACTCAACACAAACATCGATGGACGGCGGAAAATAGCCTT
TACCATCACTGCCATTAAGGGAGAGGGGGAAGGTATGCTCATGTGGTGTTGAGGAAAGCAGACATTGACCTCACCAACAG
AGCTAGGGAACTCACTGAAGATGAGGTTGAAGGTGTGATCACCATTCTGCAGAATCCACGACAGTACAAGATCCCAGACT
GGTTCTTGAACAGACAGAAGGATGTAAAGGATGGAAAACAGAGTCAGGTTCTGGCCAATGGTCTAGACAATAAACTCCGG
GAGGACCTGGAGTGACTGAAGAAGATTAGGGCCCACAGGGTACTGTGCCACTTCTGGGGCCTTCGTGTCCGAGGCCAGCA
CACTAAGACCACTGGGCGCCGAAGCCGCACCGTGGGTGTATCTAAGAAAAAA

Alignment

ORF - retro_itri_1316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGR-RYAHVVLRKADIDLTKRAGELTEDEVERVITI
          SLVIPEKFQHILRVLNTNIDGRRKIAF.ITAIKG.G..RYAHVVLRKADIDLT.RA.ELTEDEVE.VITI
Retrocopy SLVIPEKFQHILRVLNTNIDGRRKIAFTITAIKGEGE<RYAHVVLRKADIDLTNRARELTEDEVEGVITI

Parental  MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
          .QNPRQYKIPDWFLNRQKDVKDGK.SQVLANGLDNKLREDLE.LKKIRAHR.L.HFWGLRVRGQHTKTTG
Retrocopy LQNPRQYKIPDWFLNRQKDVKDGKQSQVLANGLDNKLREDLE*LKKIRAHRVLCHFWGLRVRGQHTKTTG

Parental  RRGRTVGVSKKK
          RR.RTVGVSKKK
Retrocopy RRSRTVGVSKKK

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_1316 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1316 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 16 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002918	1 retrocopy	retro_acar_206,
Ailuropoda melanoleuca	ENSAMEG00000001623	2 retrocopies	retro_amel_1617, retro_amel_381,
Cavia porcellus	ENSCPOG00000019675	4 retrocopies	retro_cpor_1044, retro_cpor_130, retro_cpor_860, retro_cpor_971,
Felis catus	ENSFCAG00000004013	7 retrocopies	retro_fcat_1058, retro_fcat_1536, retro_fcat_166, retro_fcat_222, retro_fcat_313, retro_fcat_327, retro_fcat_430,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Myotis lucifugus	ENSMLUG00000007360	2 retrocopies	retro_mluc_181, retro_mluc_932,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Mustela putorius furo	ENSMPUG00000002306	6 retrocopies	retro_mputfur_1110, retro_mputfur_1204, retro_mputfur_399, retro_mputfur_687, retro_mputfur_888, retro_mputfur_943,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,
Ictidomys tridecemlineatus	ENSSTOG00000002417	13 retrocopies	retro_itri_1023, retro_itri_1049, retro_itri_1121, retro_itri_1316 , retro_itri_1484, retro_itri_228, retro_itri_397, retro_itri_547, retro_itri_690, retro_itri_742, retro_itri_854, retro_itri_875, retro_itri_878,