RetrogeneDB ID: retro_itri_728

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393314.1:1269240..1269634(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025652
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSSTOG00000013000
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_itri_728
AATGACACAGTAACTATCTGACCAGAAAGTTCATAACCAACCAACTACTTCAGAGGAAAAAAATGGTCATTGATGTTCTT
CACCCTGGGAAAGCAACAATATCTAAGATAGAAATTCCAGAAAAATCAGTCAAATGTACGAGACCACATCAGATATCATC
TTTGTGTTTGAATTCAGAACCCATCTTGGAGGTGGCAAGACAGCTGGCTTTGGCATGATTTATGATTCCTTGGCTTATAC
AAAGAAAAATGAACCCAAACATAAACTGGCAAGACATGGCCTGTATGAAAAGAAAAAGACCTCAAGAGAACAGTGTAAGG
AACGCAAGAACAGAATGAACAAAGTCAGGGGGACTGCAAAGGCAAATGTTGGTGCTGGCAAAAAGCTAGGTGAG

Alignment

ORF - retro_itri_728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.85 %
• Parental protein coverage: 92.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NDTVTI-RTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREK-LAKMYKTTPDVIFVFGFRTHFGGGKT
          NDTVTI..TRKF.TN.LLQRK.MVIDVLHPGKAT..K.EI.EK....MY.TT.D.IFVF.FRTH.GGGKT
Retrocopy NDTVTI<LTRKFITNQLLQRKKMVIDVLHPGKATISKIEIPEK<ISQMYETTSDIIFVFEFRTHLGGGKT

Parental  TGFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKKMRE
          .GFGMIYDSL.Y.KKNEPKH.LARHGLYEKKKTSR.Q.KERKNRM.KVRGTAKANVGAGKK..E
Retrocopy AGFGMIYDSLAYTKKNEPKHKLARHGLYEKKKTSREQCKERKNRMNKVRGTAKANVGAGKKLGE

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_728 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_728 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 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013264	9 retrocopies	retro_btau_1137, retro_btau_1311, retro_btau_1562, retro_btau_285, retro_btau_467, retro_btau_577, retro_btau_586, retro_btau_788, retro_btau_980,
Dipodomys ordii	ENSDORG00000000189	4 retrocopies	retro_dord_248, retro_dord_498, retro_dord_717, retro_dord_766,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Homo sapiens	ENSG00000138326	3 retrocopies	retro_hsap_1511, retro_hsap_526, retro_hsap_658,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439, retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Mus musculus	ENSMUSG00000025290	13 retrocopies	retro_mmus_1101, retro_mmus_1462, retro_mmus_1589, retro_mmus_1592, retro_mmus_1599, retro_mmus_2134, retro_mmus_2332, retro_mmus_2497, retro_mmus_2984, retro_mmus_3162, retro_mmus_321, retro_mmus_3233, retro_mmus_602,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16,
Otolemur garnettii	ENSOGAG00000011005	3 retrocopies	retro_ogar_1000, retro_ogar_2, retro_ogar_2130,
Pan troglodytes	ENSPTRG00000002666	10 retrocopies	retro_ptro_1023, retro_ptro_1114, retro_ptro_1257, retro_ptro_1555, retro_ptro_1885, retro_ptro_2376, retro_ptro_362, retro_ptro_393, retro_ptro_478, retro_ptro_983,
Ictidomys tridecemlineatus	ENSSTOG00000013000	4 retrocopies	retro_itri_167, retro_itri_376, retro_itri_528, retro_itri_728 ,
Tarsius syrichta	ENSTSYG00000006715	1 retrocopy	retro_tsyr_1919,