RetrogeneDB ID: retro_itri_1179

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393394.1:413665..414220(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS4X
• Ensembl ID: ENSSTOG00000028692
• Aliases: None
• Description: ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]

Sequence

>retro_itri_1179
CCCAAGAACCATCTGAAGAGAGTAGTAGCTCCAAAGCAGTGGATGCTAAATAAATTGCCTAGTGTGCTTGATCTTTATTC
ATCTTCTGGTCCCTAAAAACTAATAGAAAACTTCCTTTTATATTTTTTCCTAAGGAACAGACTTAAGTATGCCCTGACAT
GAGGTGAAGTATAAAGAACATCTGCATGTAGTATTTCTTTAAGGTTGGTGGCAAAGTCTGAACTGATATAACCTACCTTG
CTGCTTTTATGGATGTCATCAGGATTTAAAAGTCCACAGATAATTTATGCCAGATTATGATACTAAGGGTCACTTTGCTG
TACATTATATTATATCTGAGGAGGTCGGGTACACATTGTATAAAATAAGAAAGAAATTGTGGGCACAGAAGTGATCCTTC
CCCTGGTGACCTATGATGCTCACATCATTCACTACCCTGCTTCCATCATCAAGGTAAATGACACCATTCAGATTAAATGG
AAGCCTGGAAAGGATATTAATTTCACCAAATTTTACACTAGTAACCTGCATATGACTACTGGAAGAATTGATCTG

Alignment

ORF - retro_itri_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.67 %
• Parental protein coverage: 70.34 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALT-GD-EVKKICMQRFIKI
          PK.HLKRV.APK.WML.KL..V.....S.GP.KL.E...L..FLRNRLKYALT.G....K.ICM..F.K.
Retrocopy PKNHLKRVVAPKQWMLNKLPSVLDLYSSSGP*KLIENFLLYFFLRNRLKYALT*GE<SIKNICM*YFFKV

Parental  DGKVRTDITYPAGFMDVISIDKTGENFRLI-YDTKGRFAVHRITPEEAKYKLCKVRKIF-VGTKGIPHLV
          .GKV.TDITY.A.FMDVI.I.K...N...I.YDTKG.FAVH.I..EE..Y.L.K.RK...VGT..I..LV
Retrocopy GGKV*TDITYLAAFMDVIRI*KSTDNLCQI<YDTKGHFAVHYIISEEVGYTLYKIRKKL<VGTEVILPLV

Parental  THDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANL
          T.DA..I.YP...IKVNDTIQI....GK...F.KF.T.NL.M.TG...L
Retrocopy TYDAHIIHYPASIIKVNDTIQIKWKPGKDINFTKFYTSNLHMTTGRIDL

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_1179 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1179 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 23 parental genes, and 150 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Ailuropoda melanoleuca	ENSAMEG00000005805	14 retrocopies	retro_amel_1003, retro_amel_1128, retro_amel_1296, retro_amel_1381, retro_amel_1695, retro_amel_1869, retro_amel_195, retro_amel_259, retro_amel_327, retro_amel_576, retro_amel_767, retro_amel_869, retro_amel_968, retro_amel_971,
Bos taurus	ENSBTAG00000018800	5 retrocopies	retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris	ENSCAFG00000017151	2 retrocopies	retro_cfam_165, retro_cfam_194,
Callithrix jacchus	ENSCJAG00000004192	2 retrocopies	retro_cjac_19, retro_cjac_361,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Felis catus	ENSFCAG00000012041	11 retrocopies	retro_fcat_1155, retro_fcat_1498, retro_fcat_1562, retro_fcat_1751, retro_fcat_1773, retro_fcat_2024, retro_fcat_229, retro_fcat_290, retro_fcat_454, retro_fcat_563, retro_fcat_766,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Gorilla gorilla	ENSGGOG00000023079	18 retrocopies	retro_ggor_1278, retro_ggor_1319, retro_ggor_1354, retro_ggor_1367, retro_ggor_1478, retro_ggor_1479, retro_ggor_1517, retro_ggor_1520, retro_ggor_1689, retro_ggor_223, retro_ggor_2676, retro_ggor_2719, retro_ggor_572, retro_ggor_711, retro_ggor_844, retro_ggor_894, retro_ggor_895, retro_ggor_939,
Loxodonta africana	ENSLAFG00000002654	4 retrocopies	retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Myotis lucifugus	ENSMLUG00000011685	5 retrocopies	retro_mluc_1638, retro_mluc_2253, retro_mluc_301, retro_mluc_536, retro_mluc_736,
Macaca mulatta	ENSMMUG00000003295	7 retrocopies	retro_mmul_1243, retro_mmul_1589, retro_mmul_1895, retro_mmul_1999, retro_mmul_2338, retro_mmul_43, retro_mmul_97,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus	ENSMUSG00000031320	13 retrocopies	retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Pongo abelii	ENSPPYG00000020462	24 retrocopies	retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586, retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325, retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes	ENSPTRG00000022025	9 retrocopies	retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Ictidomys tridecemlineatus	ENSSTOG00000028692	8 retrocopies	retro_itri_1179 , retro_itri_1607, retro_itri_291, retro_itri_306, retro_itri_368, retro_itri_495, retro_itri_738, retro_itri_985,